2023-04-26

Project Goals

  • ☒ annotate geoduck transcriptome
  • ☒ annotate geoduck tissue transcriptome (gonad, ctenidia, heart, juvenile, larvae)
  • ☒ add comparative species analysis with Mercenaria and Manila transcriptomes against geoduck transcriptome
  • ☒ make heatmaps to visualize overexpressed and underexpressed genes

What is a Geoduck?

Load Geoduck Transcriptome

salmonMatrix<-read.table(file="https://raw.githubusercontent.com/sr320/paper-geoduck-gene-exp/main/data/salmon.merged.gene_tpm.tsv", header=TRUE, sep = '\t')
names(salmonMatrix)[1]<-"target_id"
names(salmonMatrix)[2]<-"gene"

goslims<-read.csv(file="https://raw.githubusercontent.com/RobertsLab/code/master/r_projects/sam/20230328-pgen-gene_annotation-update/outputs/02-goslim-mapping/20230329-pgen-annotations-SwissProt-GO-BP_GOslim.tab", header=TRUE, sep = '\t')

pgenerosa_simple_goslims<-salmonMatrix %>% 
  left_join(goslims, by=c("gene"))

kable(pgenerosa_simple_goslims[1:5,], caption = "Pgenerosa Transcriptome")
Pgenerosa Transcriptome
target_id gene ctenidia gonad heart juvenile larvae accessions gene_id gene_name gene_description alt_gene_description all_GO_ids BP_GO_ids CC_GO_ids MF_GO_ids GOslim Term
PGEN_.00g000010 PGEN_.00g000010 0.000000 0.000000 0.000000 4.851851 3.423667 Q86IC9;Q552T5 8620183 omt5 Probable caffeoyl-CoA O-methyltransferase 1 O-methyltransferase 5 GO:0042409;GO:0046872;GO:0008757;GO:0032259 GO:0032259 GO:0042409;GO:0046872;GO:0008757 NA NA
PGEN_.00g000020 PGEN_.00g000020 0.000000 0.000000 0.000000 0.840164 0.370266 P04177 25085 Th Tyrosine 3-monooxygenase Tyrosine 3-hydroxylase GO:0030424;GO:0005737;GO:0009898;GO:0031410;GO:0030659;GO:0005829;GO:0030425;GO:0033162;GO:0005739;GO:0043005;GO:0043025;GO:0005634;GO:0043204;GO:0048471;GO:0005790;GO:0008021;GO:0043195;GO:0016597;GO:0035240;GO:0019899;GO:0008199;GO:0008198;GO:0042802;GO:0004497;GO:0019825;GO:0019904;GO:0034617;GO:0004511;GO:0015842;GO:0009887;GO:0042423;GO:0071312;GO:0071333;GO:0071363;GO:0071287;GO:0071316;GO:0071466;GO:0021987;GO:0042745;GO:0050890;GO:0042416;GO:0006585;GO:0042755;GO:0048596;GO:0042418;GO:0042462;GO:0006631;GO:0016137;GO:0007507;GO:1990384;GO:0033076;GO:0007612;GO:0007626;GO:0007617;GO:0007613;GO:0010259;GO:0042136;GO:0042421;GO:0018963;GO:0052314;GO:0008016;GO:0014823;GO:0001975;GO:0051412;GO:0051602;GO:0032355;GO:0045471;GO:0045472;GO:0070848;GO:0009635;GO:0001666;GO:0035902;GO:0017085;GO:0035900;GO:0009416;GO:0032496;GO:0010038;GO:0035094;GO:0031667;GO:0014070;GO:0043434;GO:0046684;GO:0009651;GO:0048545;GO:0009414;GO:0009410;GO:0010043;GO:0007605;GO:0035176;GO:0006665;GO:0001963;GO:0042214;GO:0007601 GO:0015842;GO:0009887;GO:0042423;GO:0071312;GO:0071333;GO:0071363;GO:0071287;GO:0071316;GO:0071466;GO:0021987;GO:0042745;GO:0050890;GO:0042416;GO:0006585;GO:0042755;GO:0048596;GO:0042418;GO:0042462;GO:0006631;GO:0016137;GO:0007507;GO:1990384;GO:0033076;GO:0007612;GO:0007626;GO:0007617;GO:0007613;GO:0010259;GO:0042136;GO:0042421;GO:0018963;GO:0052314;GO:0008016;GO:0014823;GO:0001975;GO:0051412;GO:0051602;GO:0032355;GO:0045471;GO:0045472;GO:0070848;GO:0009635;GO:0001666;GO:0035902;GO:0017085;GO:0035900;GO:0009416;GO:0032496;GO:0010038;GO:0035094;GO:0031667;GO:0014070;GO:0043434;GO:0046684;GO:0009651;GO:0048545;GO:0009414;GO:0009410;GO:0010043;GO:0007605;GO:0035176;GO:0006665;GO:0001963;GO:0042214;GO:0007601 GO:0030424;GO:0005737;GO:0009898;GO:0031410;GO:0030659;GO:0005829;GO:0030425;GO:0033162;GO:0005739;GO:0043005;GO:0043025;GO:0005634;GO:0043204;GO:0048471;GO:0005790;GO:0008021;GO:0043195 GO:0016597;GO:0035240;GO:0019899;GO:0008199;GO:0008198;GO:0042802;GO:0004497;GO:0019825;GO:0019904;GO:0034617;GO:0004511 GO:0016192;GO:0048856;GO:0048856;GO:0050877;GO:0006520;GO:0048856;GO:0030154;GO:0048856;GO:0006629;GO:1901135;GO:0048856;GO:0048856;GO:0050877;GO:0022414;GO:0050877;GO:0048856;GO:0003013;GO:0050877;GO:0006629;GO:0023052;GO:0006629;GO:0050877 vesicle-mediated transport;anatomical structure development;anatomical structure development;nervous system process;cellular amino acid metabolic process;anatomical structure development;cell differentiation;anatomical structure development;lipid metabolic process;carbohydrate derivative metabolic process;anatomical structure development;anatomical structure development;nervous system process;reproductive process;nervous system process;anatomical structure development;circulatory system process;nervous system process;lipid metabolic process;signaling;lipid metabolic process;nervous system process
PGEN_.00g000030 PGEN_.00g000030 0.225494 0.000000 0.000000 0.069598 0.052545 NA NA NA NA NA NA NA NA NA NA NA
PGEN_.00g000040 PGEN_.00g000040 0.565506 0.000000 0.254843 0.376364 1.131114 NA NA NA NA NA NA NA NA NA NA NA
PGEN_.00g000050 PGEN_.00g000050 0.508251 4.745168 0.228272 0.182728 1.117655 Q8L840;O04092;Q9FT71 837636 RECQL4A ATP-dependent DNA helicase Q-like 4A SGS1-like protein GO:0005694;GO:0005737;GO:0005634;GO:0009506;GO:0043138;GO:0005524;GO:0016887;GO:0009378;GO:0046872;GO:0003676;GO:0071215;GO:0070417;GO:0006974;GO:0051276;GO:0032508;GO:0006310;GO:0006281;GO:0006268;GO:0000724 GO:0071215;GO:0070417;GO:0006974;GO:0051276;GO:0032508;GO:0006310;GO:0006281;GO:0006268;GO:0000724 GO:0005694;GO:0005737;GO:0005634;GO:0009506 GO:0043138;GO:0005524;GO:0016887;GO:0009378;GO:0046872;GO:0003676 GO:0006260;GO:0006281;GO:0006310 DNA replication;DNA repair;DNA recombination 
##         target_id            gene ctenidia    gonad    heart juvenile   larvae
## 1 PGEN_.00g000010 PGEN_.00g000010 0.000000 0.000000 0.000000 4.851851 3.423667
## 2 PGEN_.00g000020 PGEN_.00g000020 0.000000 0.000000 0.000000 0.840164 0.370266
## 3 PGEN_.00g000030 PGEN_.00g000030 0.225494 0.000000 0.000000 0.069598 0.052545
## 4 PGEN_.00g000040 PGEN_.00g000040 0.565506 0.000000 0.254843 0.376364 1.131114
## 5 PGEN_.00g000050 PGEN_.00g000050 0.508251 4.745168 0.228272 0.182728 1.117655
## 6 PGEN_.00g000060 PGEN_.00g000060 6.490179 0.000000 0.000000 6.742646 5.936612
##         target_id            gene   tissue      tpm
## 1 PGEN_.00g000010 PGEN_.00g000010 ctenidia 0.000000
## 2 PGEN_.00g000020 PGEN_.00g000020 ctenidia 0.000000
## 3 PGEN_.00g000030 PGEN_.00g000030 ctenidia 0.225494
## 4 PGEN_.00g000040 PGEN_.00g000040 ctenidia 0.565506
## 5 PGEN_.00g000050 PGEN_.00g000050 ctenidia 0.508251
## 6 PGEN_.00g000060 PGEN_.00g000060 ctenidia 6.490179

Break cells by semi-colon and return only distinct values

#break cells and reform with unique values only
distinct_goslims <- pgenerosa_simple_goslims %>%
  mutate(Term_unique = lapply(strsplit(as.character(Term), ";"), function(Term_unique) paste0(unique(Term_unique), collapse = ";")))  %>% distinct(Term_unique, .keep_all = TRUE) %>%
  mutate(GOslim_unique = lapply(strsplit(as.character(GOslim),";"),function(GOslim_unique) paste0(unique(GOslim_unique), collapse = ";"))) %>% 
  distinct(GOslim_unique, .keep_all = TRUE)

head(distinct_goslims)
##         target_id            gene ctenidia    gonad    heart juvenile   larvae
## 1 PGEN_.00g000010 PGEN_.00g000010 0.000000 0.000000 0.000000 4.851851 3.423667
## 2 PGEN_.00g000020 PGEN_.00g000020 0.000000 0.000000 0.000000 0.840164 0.370266
## 3 PGEN_.00g000050 PGEN_.00g000050 0.508251 4.745168 0.228272 0.182728 1.117655
## 4 PGEN_.00g000060 PGEN_.00g000060 6.490179 0.000000 0.000000 6.742646 5.936612
## 5 PGEN_.00g000080 PGEN_.00g000080 0.000000 0.000000 0.119488 0.229570 0.000000
## 6 PGEN_.00g000090 PGEN_.00g000090 0.187374 0.000000 0.000000 0.173312 0.000000
##                                                    accessions gene_id gene_name
## 1                                               Q86IC9;Q552T5 8620183      omt5
## 2                                                      P04177   25085        Th
## 3                                        Q8L840;O04092;Q9FT71  837636   RECQL4A
## 4 Q61043;A0A1Y7VJL5;B2RQ73;B7ZMZ9;E9Q488;E9Q4S3;Q674R4;Q6ZPM7   18080       Nin
## 5                                                      A1E2V0  489433     BIRC3
## 6                                                      P34456  186266          
##                              gene_description
## 1 Probable caffeoyl-CoA O-methyltransferase 1
## 2                    Tyrosine 3-monooxygenase
## 3        ATP-dependent DNA helicase Q-like 4A
## 4                                      Ninein
## 5 Baculoviral IAP repeat-containing protein 3
## 6            Uncharacterized protein F54H12.2
##                       alt_gene_description
## 1                    O-methyltransferase 5
## 2                   Tyrosine 3-hydroxylase
## 3                        SGS1-like protein
## 4                        SGS1-like protein
## 5 RING-type E3 ubiquitin transferase BIRC3
## 6 RING-type E3 ubiquitin transferase BIRC3
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       all_GO_ids
## 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    GO:0042409;GO:0046872;GO:0008757;GO:0032259
## 2 GO:0030424;GO:0005737;GO:0009898;GO:0031410;GO:0030659;GO:0005829;GO:0030425;GO:0033162;GO:0005739;GO:0043005;GO:0043025;GO:0005634;GO:0043204;GO:0048471;GO:0005790;GO:0008021;GO:0043195;GO:0016597;GO:0035240;GO:0019899;GO:0008199;GO:0008198;GO:0042802;GO:0004497;GO:0019825;GO:0019904;GO:0034617;GO:0004511;GO:0015842;GO:0009887;GO:0042423;GO:0071312;GO:0071333;GO:0071363;GO:0071287;GO:0071316;GO:0071466;GO:0021987;GO:0042745;GO:0050890;GO:0042416;GO:0006585;GO:0042755;GO:0048596;GO:0042418;GO:0042462;GO:0006631;GO:0016137;GO:0007507;GO:1990384;GO:0033076;GO:0007612;GO:0007626;GO:0007617;GO:0007613;GO:0010259;GO:0042136;GO:0042421;GO:0018963;GO:0052314;GO:0008016;GO:0014823;GO:0001975;GO:0051412;GO:0051602;GO:0032355;GO:0045471;GO:0045472;GO:0070848;GO:0009635;GO:0001666;GO:0035902;GO:0017085;GO:0035900;GO:0009416;GO:0032496;GO:0010038;GO:0035094;GO:0031667;GO:0014070;GO:0043434;GO:0046684;GO:0009651;GO:0048545;GO:0009414;GO:0009410;GO:0010043;GO:0007605;GO:0035176;GO:0006665;GO:0001963;GO:0042214;GO:0007601
## 3                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               GO:0005694;GO:0005737;GO:0005634;GO:0009506;GO:0043138;GO:0005524;GO:0016887;GO:0009378;GO:0046872;GO:0003676;GO:0071215;GO:0070417;GO:0006974;GO:0051276;GO:0032508;GO:0006310;GO:0006281;GO:0006268;GO:0000724
## 4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GO:0045177;GO:0030424;GO:0044295;GO:0120103;GO:0005814;GO:0005813;GO:0097539;GO:0005881;GO:0030425;GO:0072686;GO:0097431;GO:0005730;GO:0005654;GO:0000242;GO:0005886;GO:0000922;GO:0005509;GO:0005525;GO:0019900;GO:0051011;GO:0010457;GO:0051642;GO:0090222;GO:0048668;GO:0021540;GO:0021957;GO:0034454;GO:0050772;GO:0031116;GO:0008104
## 5                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       GO:0005737;GO:0005829;GO:0005654;GO:0005634;GO:0043027;GO:0046872;GO:0061630;GO:0043066;GO:0060546;GO:0031398;GO:0051726
## 6                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               GO:0005829;GO:0004748;GO:0009263
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    BP_GO_ids
## 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 GO:0032259
## 2 GO:0015842;GO:0009887;GO:0042423;GO:0071312;GO:0071333;GO:0071363;GO:0071287;GO:0071316;GO:0071466;GO:0021987;GO:0042745;GO:0050890;GO:0042416;GO:0006585;GO:0042755;GO:0048596;GO:0042418;GO:0042462;GO:0006631;GO:0016137;GO:0007507;GO:1990384;GO:0033076;GO:0007612;GO:0007626;GO:0007617;GO:0007613;GO:0010259;GO:0042136;GO:0042421;GO:0018963;GO:0052314;GO:0008016;GO:0014823;GO:0001975;GO:0051412;GO:0051602;GO:0032355;GO:0045471;GO:0045472;GO:0070848;GO:0009635;GO:0001666;GO:0035902;GO:0017085;GO:0035900;GO:0009416;GO:0032496;GO:0010038;GO:0035094;GO:0031667;GO:0014070;GO:0043434;GO:0046684;GO:0009651;GO:0048545;GO:0009414;GO:0009410;GO:0010043;GO:0007605;GO:0035176;GO:0006665;GO:0001963;GO:0042214;GO:0007601
## 3                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         GO:0071215;GO:0070417;GO:0006974;GO:0051276;GO:0032508;GO:0006310;GO:0006281;GO:0006268;GO:0000724
## 4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              GO:0010457;GO:0051642;GO:0090222;GO:0048668;GO:0021540;GO:0021957;GO:0034454;GO:0050772;GO:0031116;GO:0008104
## 5                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                GO:0043066;GO:0060546;GO:0031398;GO:0051726
## 6                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 GO:0009263
##                                                                                                                                                                                    CC_GO_ids
## 1                                                                                                                                                                                           
## 2 GO:0030424;GO:0005737;GO:0009898;GO:0031410;GO:0030659;GO:0005829;GO:0030425;GO:0033162;GO:0005739;GO:0043005;GO:0043025;GO:0005634;GO:0043204;GO:0048471;GO:0005790;GO:0008021;GO:0043195
## 3                                                                                                                                                GO:0005694;GO:0005737;GO:0005634;GO:0009506
## 4            GO:0045177;GO:0030424;GO:0044295;GO:0120103;GO:0005814;GO:0005813;GO:0097539;GO:0005881;GO:0030425;GO:0072686;GO:0097431;GO:0005730;GO:0005654;GO:0000242;GO:0005886;GO:0000922
## 5                                                                                                                                                GO:0005737;GO:0005829;GO:0005654;GO:0005634
## 6                                                                                                                                                                                 GO:0005829
##                                                                                                                  MF_GO_ids
## 1                                                                                         GO:0042409;GO:0046872;GO:0008757
## 2 GO:0016597;GO:0035240;GO:0019899;GO:0008199;GO:0008198;GO:0042802;GO:0004497;GO:0019825;GO:0019904;GO:0034617;GO:0004511
## 3                                                        GO:0043138;GO:0005524;GO:0016887;GO:0009378;GO:0046872;GO:0003676
## 4                                                                              GO:0005509;GO:0005525;GO:0019900;GO:0051011
## 5                                                                                         GO:0043027;GO:0046872;GO:0061630
## 6                                                                                                               GO:0004748
##                                                                                                                                                                                                                                              GOslim
## 1                                                                                                                                                                                                                                              <NA>
## 2 GO:0016192;GO:0048856;GO:0048856;GO:0050877;GO:0006520;GO:0048856;GO:0030154;GO:0048856;GO:0006629;GO:1901135;GO:0048856;GO:0048856;GO:0050877;GO:0022414;GO:0050877;GO:0048856;GO:0003013;GO:0050877;GO:0006629;GO:0023052;GO:0006629;GO:0050877
## 3                                                                                                                                                                                                                  GO:0006260;GO:0006281;GO:0006310
## 4                                                                                         GO:0007010;GO:0007010;GO:0065003;GO:0030154;GO:0048856;GO:0030154;GO:0048856;GO:0030154;GO:0048856;GO:0007010;GO:0030154;GO:0048856;GO:0007010;GO:0065003
## 5                                                                                                                                                                                                                             GO:0012501;GO:0012501
## 6                                                                                                                                                                                                                             GO:0055086;GO:1901135
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Term
## 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <NA>
## 2 vesicle-mediated transport;anatomical structure development;anatomical structure development;nervous system process;cellular amino acid metabolic process;anatomical structure development;cell differentiation;anatomical structure development;lipid metabolic process;carbohydrate derivative metabolic process;anatomical structure development;anatomical structure development;nervous system process;reproductive process;nervous system process;anatomical structure development;circulatory system process;nervous system process;lipid metabolic process;signaling;lipid metabolic process;nervous system process
## 3                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                DNA replication;DNA repair;DNA recombination
## 4                                                                                                                                                                                                                     cytoskeleton organization;cytoskeleton organization;protein-containing complex assembly;cell differentiation;anatomical structure development;cell differentiation;anatomical structure development;cell differentiation;anatomical structure development;cytoskeleton organization;cell differentiation;anatomical structure development;cytoskeleton organization;protein-containing complex assembly
## 5                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 programmed cell death;programmed cell death
## 6                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            nucleobase-containing small molecule metabolic process;carbohydrate derivative metabolic process
##                                                                                                                                                                                                                                                                 Term_unique
## 1                                                                                                                                                                                                                                                                        NA
## 2 vesicle-mediated transport;anatomical structure development;nervous system process;cellular amino acid metabolic process;cell differentiation;lipid metabolic process;carbohydrate derivative metabolic process;reproductive process;circulatory system process;signaling
## 3                                                                                                                                                                                                                              DNA replication;DNA repair;DNA recombination
## 4                                                                                                                                                       cytoskeleton organization;protein-containing complex assembly;cell differentiation;anatomical structure development
## 5                                                                                                                                                                                                                                                     programmed cell death
## 6                                                                                                                                                                          nucleobase-containing small molecule metabolic process;carbohydrate derivative metabolic process
##                                                                                                   GOslim_unique
## 1                                                                                                            NA
## 2 GO:0016192;GO:0048856;GO:0050877;GO:0006520;GO:0030154;GO:0006629;GO:1901135;GO:0022414;GO:0003013;GO:0023052
## 3                                                                              GO:0006260;GO:0006281;GO:0006310
## 4                                                                   GO:0007010;GO:0065003;GO:0030154;GO:0048856
## 5                                                                                                    GO:0012501
## 6                                                                                         GO:0055086;GO:1901135

Get GOterm counts

#count top GOterms
tissue_goslims <- pgenerosa_long %>%
    group_by(tissue) %>% 
  filter(binary == 1) %>%
  mutate(Term_unique = lapply(strsplit(as.character(Term), ";"), function(Term_unique) paste0(unique(Term_unique), collapse = ";"))) %>% 
  distinct(Term_unique, .keep_all = TRUE) %>% 
  filter(!is.na(Term_unique)) %>%
  separate_rows(Term_unique, sep = ";") %>%
  mutate(Term_unique = trimws(Term_unique)) %>%
  count(Term_unique, tissue, sort = TRUE)

kable(tissue_goslims[1:5,], caption="GOterms by tissue")
GOterms by tissue
tissue Term_unique n
juvenile anatomical structure development 1817
larvae anatomical structure development 1743
heart anatomical structure development 1678
ctenidia anatomical structure development 1661
juvenile signaling 1572

SPECIES

  • download blast from Mercenaria or Manila Clams against Pgenerosa db
gene Scaffold Mercenaria_gene V3 V4 V5 V6 V7 V8 V9 V10 e-value V12
PGEN_.00g000040 Scaffold_01:55792-67546 XM_045314054.2 84.706 170 26 0 10212 10381 1425 1594 0 171
PGEN_.00g000050 Scaffold_01:67586-69113 XM_053546612.1 83.056 602 80 10 3 583 1058 458 0 527
PGEN_.00g000060 Scaffold_01:70713-81099 XM_053526799.1 75.616 406 85 8 8332 8725 7243 7646 0 189
PGEN_.00g000270 Scaffold_01:344820-379444 XM_053526799.1 76.190 609 125 19 12681 13279 7048 7646 0 303
PGEN_.00g000280 Scaffold_01:402378-436712 XR_008368031.1 83.088 136 18 4 19326 19461 2938 3068 0 119
PGEN_.00g000300 Scaffold_01:503707-557915 XR_008366499.1 83.871 186 25 4 2983 3165 1180 997 0 172
PGEN_.00g000440 Scaffold_01:868194-911401 XM_053546296.1 81.250 320 39 12 33926 34225 1418 1100 0 239
PGEN_.00g000460 Scaffold_01:936602-978401 XM_053532133.1 83.721 215 33 2 26135 26348 1757 1544 0 202
PGEN_.00g000480 Scaffold_01:1018280-1021447 XM_045316439.2 83.810 210 33 1 629 838 9625 9417 0 198
PGEN_.00g000490 Scaffold_01:1042400-1066675 XM_053551149.1 83.704 135 17 5 18812 18943 7341 7209 0 122
PGEN_.00g000520 Scaffold_01:1105662-1112517 XR_008372115.1 87.586 145 18 0 6258 6402 8529 8673 0 169
PGEN_.00g000530 Scaffold_01:1119467-1128894 XR_008369200.1 84.651 215 33 0 1759 1973 677 463 0 215
PGEN_.00g000670 Scaffold_01:1389639-1400328 XM_045303199.2 82.298 322 57 0 5424 5745 2280 1959 0 279
PGEN_.00g000680 Scaffold_01:1402133-1405997 XM_045316591.2 88.073 218 26 0 3083 3300 6336 6119 0 259
PGEN_.00g000790 Scaffold_01:1558681-1570002 XR_008372115.1 85.253 217 32 0 1446 1662 8729 8513 0 224
PGEN_.00g000970 Scaffold_01:1970367-1991359 XM_045304273.2 88.696 115 12 1 17344 17458 665 552 0 139
PGEN_.00g000980 Scaffold_01:2015518-2047143 XM_053546296.1 88.318 214 25 0 7396 7609 1314 1101 0 257
PGEN_.00g001000 Scaffold_01:2058418-2067040 XM_053538492.1 82.870 216 32 4 3819 4032 4581 4369 0 189
PGEN_.00g001030 Scaffold_01:2129680-2143865 XM_045310265.2 84.932 219 26 5 11306 11523 2989 2777 0 215
PGEN_.00g001080 Scaffold_01:2184093-2211336 XM_045304994.2 79.336 271 50 4 20430 20695 1876 1607 0 185
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PGEN_.00g346970 Scaffold_18:20710613-20730196 XM_053532133.1 87.895 190 23 0 5345 5534 1568 1757 0 224
PGEN_.00g347020 Scaffold_18:20773250-20789855 XM_053537037.1 82.514 183 29 3 9057 9236 6898 6716 0 158
PGEN_.00g347040 Scaffold_18:20957623-20975489 XM_053546296.1 84.118 170 27 0 11821 11990 1138 1307 0 165
PGEN_.00g347160 Scaffold_18:21606111-21670307 XM_053546296.1 86.344 227 29 2 10735 10961 1094 1318 0 246
PGEN_.00g347170 Scaffold_18:21678191-21704069 XM_053546296.1 86.977 215 28 0 23372 23586 1314 1100 0 243
PGEN_.00g347480 Scaffold_18:22269329-22290069 XM_053532133.1 86.341 205 22 3 6079 6277 1558 1762 0 219
PGEN_.00g347580 Scaffold_18:22435815-22453283 XM_053546296.1 86.538 208 28 0 15694 15901 1307 1100 0 230
PGEN_.00g347600 Scaffold_18:22474032-22483886 XR_008366376.1 90.909 88 3 4 8462 8545 1695 1781 0 113
PGEN_.00g347610 Scaffold_18:22486595-22513371 XM_053537037.1 80.602 299 42 11 15812 16094 6984 6686 0 217
PGEN_.00g347630 Scaffold_18:22662533-22693622 XM_053530899.1 83.582 134 22 0 16482 16615 1185 1318 0 126
PGEN_.00g347690 Scaffold_18:22780768-22802518 XM_045357830.2 77.703 296 55 10 11577 11864 3294 3002 0 171
PGEN_.00g347750 Scaffold_18:22923652-22926778 XM_045351850.2 91.111 90 5 3 789 878 6171 6257 0 119
PGEN_.00g347890 Scaffold_18:23285051-23301363 XM_053548246.1 89.216 102 9 2 12671 12772 3756 3657 0 126
PGEN_.00g347900 Scaffold_18:23302157-23317099 XM_045316439.2 86.538 208 28 0 5509 5716 9619 9412 0 230
PGEN_.00g347960 Scaffold_18:23571295-23584415 XM_053546296.1 86.383 235 31 1 2301 2534 1314 1080 0 255
PGEN_.00g348010 Scaffold_18:23726427-23735785 XM_053546296.1 86.036 222 29 2 764 983 1307 1086 0 237
PGEN_.00g348020 Scaffold_18:23740425-23749271 XM_053532893.1 81.279 219 32 7 5014 5232 1103 1312 0 169
PGEN_.00g348040 Scaffold_18:23773260-23787096 XM_053518352.1 80.000 305 43 10 7187 7473 2338 2034 0 209
PGEN_.00g348110 Scaffold_18:23918721-23929110 XM_045360842.2 77.928 222 46 2 2999 3218 7371 7151 0 135
PGEN_.00g348160 Scaffold_18:24073533-24123087 XM_045357830.2 77.739 283 46 11 31583 31849 3002 3283 0 158
PGEN_.00g348310 Scaffold_18:24404224-24407426 XM_053520372.1 88.811 143 10 6 1682 1820 179 39 0 171
PGEN_.00g348350 Scaffold_18:24468192-24501453 XR_008372115.1 87.850 214 25 1 22010 22222 8517 8730 0 250
PGEN_.00g348400 Scaffold_18:24630997-24692928 XM_045360842.2 76.694 605 112 21 32586 33167 7746 7148 0 309
PGEN_.00g348410 Scaffold_18:24708032-24770271 XM_045360842.2 76.694 605 112 21 29072 29653 7148 7746 0 309
PGEN_.00g348460 Scaffold_18:24899205-24932487 XR_008372115.1 87.850 214 25 1 11038 11250 8730 8517 0 250
PGEN_.00g348500 Scaffold_18:24993254-24996452 XM_053520372.1 88.811 143 10 6 1360 1498 39 179 0 171
PGEN_.00g348610 Scaffold_18:25321168-25365174 XM_053520372.1 86.131 137 9 7 29957 30084 179 44 0 139
PGEN_.00g348630 Scaffold_18:25449228-25478297 XM_045357017.2 80.374 214 33 3 21700 21906 6491 6702 0 154
PGEN_.00g348850 Scaffold_18:25874793-25895881 XM_045300827.2 88.197 1525 140 17 13058 14559 3383 1876 0 1783
PGEN_.00g349420 Scaffold_18:27616208-27641361 XM_045357855.2 87.500 104 9 4 18517 18619 4600 4500 0 117
PGEN_.00g349440 Scaffold_18:27686936-27710873 XM_053516544.1 74.415 641 142 14 4422 5044 10280 10916 0 255

ex) Annotated Mercenaria Transcriptome

#join clam transcriptome with goslims
Manila_Pgen_goslims <- Manila_Pgen_new %>%
left_join(goslims, by=c("gene"))
Pgen_Manila_goslims <- Pgen_Manila_new %>%
  left_join(goslims, by=c("gene"))
Mercenaria_Pgen_goslims<- Mercenaria_Pgen_new %>%
left_join(goslims, by=c("gene")) #6521
Pgen_Mercenaria_goslims<- Pgen_Mercenaria_new %>%
left_join(goslims, by=c("gene")) #5099
kable(Pgen_Mercenaria_goslims[1:5,], caption="annotated Mercenaria Transcriptome")
annotated Mercenaria Transcriptome
gene Scaffold Mercenaria_gene V3 V4 V5 V6 V7 V8 V9 V10 e-value V12 accessions gene_id gene_name gene_description alt_gene_description all_GO_ids BP_GO_ids CC_GO_ids MF_GO_ids GOslim Term
PGEN_.00g000040 Scaffold_01:55792-67546 XM_045314054.2 84.706 170 26 0 10212 10381 1425 1594 0 171 NA NA NA NA NA NA NA NA NA NA NA
PGEN_.00g000050 Scaffold_01:67586-69113 XM_053546612.1 83.056 602 80 10 3 583 1058 458 0 527 Q8L840;O04092;Q9FT71 837636 RECQL4A ATP-dependent DNA helicase Q-like 4A SGS1-like protein GO:0005694;GO:0005737;GO:0005634;GO:0009506;GO:0043138;GO:0005524;GO:0016887;GO:0009378;GO:0046872;GO:0003676;GO:0071215;GO:0070417;GO:0006974;GO:0051276;GO:0032508;GO:0006310;GO:0006281;GO:0006268;GO:0000724 GO:0071215;GO:0070417;GO:0006974;GO:0051276;GO:0032508;GO:0006310;GO:0006281;GO:0006268;GO:0000724 GO:0005694;GO:0005737;GO:0005634;GO:0009506 GO:0043138;GO:0005524;GO:0016887;GO:0009378;GO:0046872;GO:0003676 GO:0006260;GO:0006281;GO:0006310 DNA replication;DNA repair;DNA recombination
PGEN_.00g000060 Scaffold_01:70713-81099 XM_053526799.1 75.616 406 85 8 8332 8725 7243 7646 0 189 Q61043;A0A1Y7VJL5;B2RQ73;B7ZMZ9;E9Q488;E9Q4S3;Q674R4;Q6ZPM7 18080 Nin Ninein SGS1-like protein GO:0045177;GO:0030424;GO:0044295;GO:0120103;GO:0005814;GO:0005813;GO:0097539;GO:0005881;GO:0030425;GO:0072686;GO:0097431;GO:0005730;GO:0005654;GO:0000242;GO:0005886;GO:0000922;GO:0005509;GO:0005525;GO:0019900;GO:0051011;GO:0010457;GO:0051642;GO:0090222;GO:0048668;GO:0021540;GO:0021957;GO:0034454;GO:0050772;GO:0031116;GO:0008104 GO:0010457;GO:0051642;GO:0090222;GO:0048668;GO:0021540;GO:0021957;GO:0034454;GO:0050772;GO:0031116;GO:0008104 GO:0045177;GO:0030424;GO:0044295;GO:0120103;GO:0005814;GO:0005813;GO:0097539;GO:0005881;GO:0030425;GO:0072686;GO:0097431;GO:0005730;GO:0005654;GO:0000242;GO:0005886;GO:0000922 GO:0005509;GO:0005525;GO:0019900;GO:0051011 GO:0007010;GO:0007010;GO:0065003;GO:0030154;GO:0048856;GO:0030154;GO:0048856;GO:0030154;GO:0048856;GO:0007010;GO:0030154;GO:0048856;GO:0007010;GO:0065003 cytoskeleton organization;cytoskeleton organization;protein-containing complex assembly;cell differentiation;anatomical structure development;cell differentiation;anatomical structure development;cell differentiation;anatomical structure development;cytoskeleton organization;cell differentiation;anatomical structure development;cytoskeleton organization;protein-containing complex assembly
PGEN_.00g000270 Scaffold_01:344820-379444 XM_053526799.1 76.190 609 125 19 12681 13279 7048 7646 0 303 NA NA NA NA NA NA NA NA NA NA NA
PGEN_.00g000280 Scaffold_01:402378-436712 XR_008368031.1 83.088 136 18 4 19326 19461 2938 3068 0 119 Q8ZXT3 NA Uncharacterized protein PAE1111 RING finger protein 84 NA NA

View GOterm counts by Species

P. generosa
Term_unique n
anatomical structure development 1853
signaling 1603
cell differentiation 1281
DNA-templated transcription 741
regulation of DNA-templated transcription 678

GOterm counts for all Pgenerosa genes

kable(term_count_best[1:10,], caption="GOterms count, removing duplicates")
GOterms count, removing duplicates
transcriptome Term_unique n
Pgenerosa anatomical structure development 1853
Pgenerosa signaling 1603
Pgenerosa cell differentiation 1281
Pgenerosa DNA-templated transcription 741
Pgenerosa regulation of DNA-templated transcription 678
Pgenerosa immune system process 670
Pgenerosa programmed cell death 600
Pgenerosa cell motility 595
Pgenerosa reproductive process 536
Pgenerosa cytoskeleton organization 516
Total Terms per Species
transcriptome total_n
Manila 1235
Manila_r 1390
Mercenaria 2198
Mercenaria_r 7027
Pgenerosa 17611
NA NA
NA NA
Species Normalized by Pgenerosa Transcriptome
transcriptome Term_unique n_species n_divided n_Pgen
Manila anatomical structure development 129 0.1044534 1853
Manila signaling 113 0.0914980 1603
Manila cell differentiation 86 0.0696356 1281
Manila cytoskeleton organization 65 0.0526316 516
Manila DNA-templated transcription 51 0.0412955 741
Manila reproductive process 48 0.0388664 536
Manila regulation of DNA-templated transcription 47 0.0380567 678
Manila cell motility 40 0.0323887 595
Manila programmed cell death 40 0.0323887 600
Manila protein-containing complex assembly 39 0.0315789 444
Manila immune system process 36 0.0291498 670
Manila mitotic cell cycle 33 0.0267206 363
Manila vesicle-mediated transport 29 0.0234818 484
Manila cilium organization 28 0.0226721 178
Manila protein catabolic process 28 0.0226721 302
Manila nervous system process 27 0.0218623 358
Manila microtubule-based movement 25 0.0202429 161
Manila mRNA metabolic process 23 0.0186235 197
Manila transmembrane transport 21 0.0170040 330
Manila cell adhesion 18 0.0145749 387
Manila carbohydrate derivative metabolic process 17 0.0137652 301
Manila DNA repair 16 0.0129555 181
Manila cell junction organization 16 0.0129555 279
Manila membrane organization 15 0.0121457 278
Manila nucleobase-containing small molecule metabolic process 15 0.0121457 172
Manila lipid metabolic process 14 0.0113360 352
Manila autophagy 12 0.0097166 161
Manila chromosome segregation 12 0.0097166 140
Manila defense response to other organism 12 0.0097166 294
Manila generation of precursor metabolites and energy 11 0.0089069 105
Manila cytokinesis 10 0.0080972 96
Manila mitotic nuclear division 10 0.0080972 132
Manila chromatin organization 9 0.0072874 115
Manila establishment or maintenance of cell polarity 9 0.0072874 105
Manila intracellular protein transport 9 0.0072874 219
Manila DNA recombination 8 0.0064777 124
Manila DNA replication 8 0.0064777 102
Manila circulatory system process 8 0.0064777 189
Manila ribosome biogenesis 8 0.0064777 69
Manila carbohydrate metabolic process 7 0.0056680 159
Manila cellular amino acid metabolic process 7 0.0056680 88
Manila nucleocytoplasmic transport 7 0.0056680 108
Manila muscle system process 6 0.0048583 127
Manila protein localization to plasma membrane 6 0.0048583 68
Manila telomere organization 6 0.0048583 80
Manila gene silencing by RNA 5 0.0040486 34
Manila inflammatory response 5 0.0040486 135
Manila mitochondrion organization 5 0.0040486 168
Manila cellular modified amino acid metabolic process 4 0.0032389 76
Manila sulfur compound metabolic process 4 0.0032389 109
Manila tRNA metabolic process 4 0.0032389 40
Manila cytoplasmic translation 3 0.0024291 17
Manila meiotic nuclear division 3 0.0024291 79
Manila wound healing 3 0.0024291 97
Manila extracellular matrix organization 2 0.0016194 58
Manila protein folding 2 0.0016194 29
Manila protein maturation 2 0.0016194 107
Manila snRNA metabolic process 2 0.0016194 16
Manila NA 1 0.0008097 1
Manila detoxification 1 0.0008097 18
Manila lysosome organization 1 0.0008097 16
Manila nitrogen cycle metabolic process 1 0.0008097 6
Manila protein glycosylation 1 0.0008097 55
Manila renal system process 1 0.0008097 48
Manila respiratory system process 1 0.0008097 17
Manila_r anatomical structure development 149 0.1071942 1853
Manila_r signaling 126 0.0906475 1603
Manila_r cell differentiation 96 0.0690647 1281
Manila_r cytoskeleton organization 68 0.0489209 516
Manila_r DNA-templated transcription 60 0.0431655 741
Manila_r regulation of DNA-templated transcription 55 0.0395683 678
Manila_r reproductive process 55 0.0395683 536
Manila_r programmed cell death 44 0.0316547 600
Manila_r immune system process 42 0.0302158 670
Manila_r protein-containing complex assembly 42 0.0302158 444
Manila_r cell motility 41 0.0294964 595
Manila_r mitotic cell cycle 36 0.0258993 363
Manila_r vesicle-mediated transport 35 0.0251799 484
Manila_r nervous system process 32 0.0230216 358
Manila_r protein catabolic process 31 0.0223022 302
Manila_r cilium organization 30 0.0215827 178
Manila_r microtubule-based movement 27 0.0194245 161
Manila_r mRNA metabolic process 26 0.0187050 197
Manila_r transmembrane transport 25 0.0179856 330
Manila_r cell adhesion 21 0.0151079 387
Manila_r cell junction organization 20 0.0143885 279
Manila_r DNA repair 19 0.0136691 181
Manila_r carbohydrate derivative metabolic process 17 0.0122302 301
Manila_r lipid metabolic process 17 0.0122302 352
Manila_r membrane organization 17 0.0122302 278
Manila_r defense response to other organism 16 0.0115108 294
Manila_r nucleobase-containing small molecule metabolic process 15 0.0107914 172
Manila_r cytokinesis 13 0.0093525 96
Manila_r autophagy 12 0.0086331 161
Manila_r chromosome segregation 12 0.0086331 140
Manila_r generation of precursor metabolites and energy 12 0.0086331 105
Manila_r DNA replication 11 0.0079137 102
Manila_r chromatin organization 11 0.0079137 115
Manila_r circulatory system process 10 0.0071942 189
Manila_r establishment or maintenance of cell polarity 10 0.0071942 105
Manila_r intracellular protein transport 10 0.0071942 219
Manila_r DNA recombination 9 0.0064748 124
Manila_r cellular amino acid metabolic process 9 0.0064748 88
Manila_r mitotic nuclear division 9 0.0064748 132
Manila_r nucleocytoplasmic transport 8 0.0057554 108
Manila_r ribosome biogenesis 8 0.0057554 69
Manila_r carbohydrate metabolic process 7 0.0050360 159
Manila_r protein localization to plasma membrane 7 0.0050360 68
Manila_r gene silencing by RNA 6 0.0043165 34
Manila_r inflammatory response 6 0.0043165 135
Manila_r mitochondrion organization 6 0.0043165 168
Manila_r muscle system process 6 0.0043165 127
Manila_r telomere organization 6 0.0043165 80
Manila_r sulfur compound metabolic process 5 0.0035971 109
Manila_r cellular modified amino acid metabolic process 4 0.0028777 76
Manila_r cytoplasmic translation 4 0.0028777 17
Manila_r meiotic nuclear division 4 0.0028777 79
Manila_r tRNA metabolic process 4 0.0028777 40
Manila_r snRNA metabolic process 3 0.0021583 16
Manila_r wound healing 3 0.0021583 97
Manila_r extracellular matrix organization 2 0.0014388 58
Manila_r protein folding 2 0.0014388 29
Manila_r protein maturation 2 0.0014388 107
Manila_r NA 1 0.0007194 1
Manila_r detoxification 1 0.0007194 18
Manila_r lysosome organization 1 0.0007194 16
Manila_r nitrogen cycle metabolic process 1 0.0007194 6
Manila_r protein glycosylation 1 0.0007194 55
Manila_r renal system process 1 0.0007194 48
Manila_r respiratory system process 1 0.0007194 17
Mercenaria anatomical structure development 247 0.1123749 1853
Mercenaria signaling 189 0.0859873 1603
Mercenaria cell differentiation 170 0.0773430 1281
Mercenaria DNA-templated transcription 88 0.0400364 741
Mercenaria cytoskeleton organization 87 0.0395814 516
Mercenaria cell motility 83 0.0377616 595
Mercenaria regulation of DNA-templated transcription 82 0.0373066 678
Mercenaria reproductive process 71 0.0323021 536
Mercenaria immune system process 66 0.0300273 670
Mercenaria programmed cell death 63 0.0286624 600
Mercenaria vesicle-mediated transport 62 0.0282075 484
Mercenaria protein-containing complex assembly 58 0.0263876 444
Mercenaria nervous system process 48 0.0218380 358
Mercenaria mitotic cell cycle 47 0.0213831 363
Mercenaria cilium organization 46 0.0209281 178
Mercenaria cell adhesion 44 0.0200182 387
Mercenaria lipid metabolic process 40 0.0181984 352
Mercenaria protein catabolic process 39 0.0177434 302
Mercenaria carbohydrate derivative metabolic process 38 0.0172884 301
Mercenaria microtubule-based movement 37 0.0168335 161
Mercenaria cell junction organization 36 0.0163785 279
Mercenaria membrane organization 35 0.0159236 278
Mercenaria transmembrane transport 34 0.0154686 330
Mercenaria DNA repair 30 0.0136488 181
Mercenaria mRNA metabolic process 28 0.0127389 197
Mercenaria intracellular protein transport 24 0.0109190 219
Mercenaria defense response to other organism 23 0.0104641 294
Mercenaria carbohydrate metabolic process 22 0.0100091 159
Mercenaria nucleobase-containing small molecule metabolic process 22 0.0100091 172
Mercenaria circulatory system process 21 0.0095541 189
Mercenaria autophagy 20 0.0090992 161
Mercenaria cytokinesis 19 0.0086442 96
Mercenaria establishment or maintenance of cell polarity 17 0.0077343 105
Mercenaria chromatin organization 16 0.0072793 115
Mercenaria nucleocytoplasmic transport 16 0.0072793 108
Mercenaria DNA recombination 15 0.0068244 124
Mercenaria chromosome segregation 15 0.0068244 140
Mercenaria DNA replication 14 0.0063694 102
Mercenaria generation of precursor metabolites and energy 14 0.0063694 105
Mercenaria protein localization to plasma membrane 14 0.0063694 68
Mercenaria cellular amino acid metabolic process 11 0.0050045 88
Mercenaria mitochondrion organization 11 0.0050045 168
Mercenaria mitotic nuclear division 11 0.0050045 132
Mercenaria inflammatory response 10 0.0045496 135
Mercenaria sulfur compound metabolic process 10 0.0045496 109
Mercenaria protein maturation 9 0.0040946 107
Mercenaria tRNA metabolic process 9 0.0040946 40
Mercenaria muscle system process 8 0.0036397 127
Mercenaria telomere organization 8 0.0036397 80
Mercenaria cytoplasmic translation 6 0.0027298 17
Mercenaria extracellular matrix organization 6 0.0027298 58
Mercenaria protein glycosylation 6 0.0027298 55
Mercenaria cellular modified amino acid metabolic process 5 0.0022748 76
Mercenaria gene silencing by RNA 5 0.0022748 34
Mercenaria meiotic nuclear division 5 0.0022748 79
Mercenaria ribosome biogenesis 5 0.0022748 69
Mercenaria endocrine process 4 0.0018198 32
Mercenaria vitamin metabolic process 4 0.0018198 38
Mercenaria wound healing 4 0.0018198 97
Mercenaria lysosome organization 3 0.0013649 16
Mercenaria mitochondrial gene expression 3 0.0013649 25
Mercenaria nitrogen cycle metabolic process 3 0.0013649 6
Mercenaria detoxification 2 0.0009099 18
Mercenaria digestive system process 2 0.0009099 41
Mercenaria renal system process 2 0.0009099 48
Mercenaria respiratory system process 2 0.0009099 17
Mercenaria snRNA metabolic process 2 0.0009099 16
Mercenaria NA 1 0.0004550 1
Mercenaria peroxisome organization 1 0.0004550 15
Mercenaria_r anatomical structure development 768 0.1092927 1853
Mercenaria_r signaling 635 0.0903657 1603
Mercenaria_r cell differentiation 517 0.0735734 1281
Mercenaria_r DNA-templated transcription 267 0.0379963 741
Mercenaria_r regulation of DNA-templated transcription 245 0.0348655 678
Mercenaria_r cell motility 241 0.0342963 595
Mercenaria_r cytoskeleton organization 237 0.0337271 516
Mercenaria_r immune system process 232 0.0330155 670
Mercenaria_r programmed cell death 229 0.0325886 600
Mercenaria_r vesicle-mediated transport 218 0.0310232 484
Mercenaria_r reproductive process 202 0.0287463 536
Mercenaria_r protein-containing complex assembly 174 0.0247616 444
Mercenaria_r cell adhesion 163 0.0231962 387
Mercenaria_r nervous system process 153 0.0217732 358
Mercenaria_r lipid metabolic process 152 0.0216309 352
Mercenaria_r mitotic cell cycle 142 0.0202078 363
Mercenaria_r transmembrane transport 133 0.0189270 330
Mercenaria_r carbohydrate derivative metabolic process 131 0.0186424 301
Mercenaria_r membrane organization 118 0.0167924 278
Mercenaria_r cell junction organization 114 0.0162231 279
Mercenaria_r protein catabolic process 111 0.0157962 302
Mercenaria_r defense response to other organism 101 0.0143731 294
Mercenaria_r cilium organization 99 0.0140885 178
Mercenaria_r intracellular protein transport 85 0.0120962 219
Mercenaria_r DNA repair 82 0.0116693 181
Mercenaria_r mRNA metabolic process 81 0.0115270 197
Mercenaria_r carbohydrate metabolic process 77 0.0109577 159
Mercenaria_r microtubule-based movement 76 0.0108154 161
Mercenaria_r nucleobase-containing small molecule metabolic process 74 0.0105308 172
Mercenaria_r circulatory system process 70 0.0099616 189
Mercenaria_r autophagy 63 0.0089654 161
Mercenaria_r mitochondrion organization 60 0.0085385 168
Mercenaria_r chromosome segregation 53 0.0075423 140
Mercenaria_r DNA recombination 52 0.0074000 124
Mercenaria_r chromatin organization 48 0.0068308 115
Mercenaria_r generation of precursor metabolites and energy 46 0.0065462 105
Mercenaria_r DNA replication 45 0.0064039 102
Mercenaria_r nucleocytoplasmic transport 44 0.0062616 108
Mercenaria_r inflammatory response 43 0.0061193 135
Mercenaria_r mitotic nuclear division 43 0.0061193 132
Mercenaria_r cytokinesis 42 0.0059769 96
Mercenaria_r muscle system process 42 0.0059769 127
Mercenaria_r sulfur compound metabolic process 42 0.0059769 109
Mercenaria_r establishment or maintenance of cell polarity 41 0.0058346 105
Mercenaria_r protein localization to plasma membrane 41 0.0058346 68
Mercenaria_r cellular amino acid metabolic process 38 0.0054077 88
Mercenaria_r protein maturation 38 0.0054077 107
Mercenaria_r cellular modified amino acid metabolic process 30 0.0042692 76
Mercenaria_r meiotic nuclear division 30 0.0042692 79
Mercenaria_r wound healing 30 0.0042692 97
Mercenaria_r ribosome biogenesis 25 0.0035577 69
Mercenaria_r telomere organization 25 0.0035577 80
Mercenaria_r protein glycosylation 23 0.0032731 55
Mercenaria_r tRNA metabolic process 19 0.0027039 40
Mercenaria_r extracellular matrix organization 16 0.0022769 58
Mercenaria_r gene silencing by RNA 15 0.0021346 34
Mercenaria_r protein folding 15 0.0021346 29
Mercenaria_r cytoplasmic translation 12 0.0017077 17
Mercenaria_r endocrine process 12 0.0017077 32
Mercenaria_r vitamin metabolic process 12 0.0017077 38
Mercenaria_r renal system process 10 0.0014231 48
Mercenaria_r respiratory system process 8 0.0011385 17
Mercenaria_r lysosome organization 7 0.0009962 16
Mercenaria_r detoxification 6 0.0008538 18
Mercenaria_r digestive system process 6 0.0008538 41
Mercenaria_r mitochondrial gene expression 4 0.0005692 25
Mercenaria_r nitrogen cycle metabolic process 4 0.0005692 6
Mercenaria_r snRNA metabolic process 4 0.0005692 16
Mercenaria_r peroxisome organization 3 0.0004269 15
Mercenaria_r cell wall organization or biogenesis 2 0.0002846 13
Mercenaria_r NA 1 0.0001423 1

Normalize Species by Pgenerosa transcriptome

filtered_data1 <- term_count_best %>%
  filter(transcriptome %in% c("Mercenaria_r", "Manila", "Mercenaria", "Manila_r")) %>%
  mutate(n_divided = case_when(
                               transcriptome == "Manila" ~ n/1235,
                               transcriptome == "Manila_r" ~ n/1390,
                               transcriptome == "Mercenaria" ~ n/2198,
                               transcriptome == "Mercenaria_r" ~ n/7027))

kable(species_normal[1:5],caption="Species Normalized by Pgenerosa Transcriptome")
Species Normalized by Pgenerosa Transcriptome
transcriptome Term_unique n_species n_divided n_Pgen
Manila anatomical structure development 129 0.1044534 1853
Manila signaling 113 0.0914980 1603
Manila cell differentiation 86 0.0696356 1281
Manila cytoskeleton organization 65 0.0526316 516
Manila DNA-templated transcription 51 0.0412955 741
Manila reproductive process 48 0.0388664 536
Manila regulation of DNA-templated transcription 47 0.0380567 678
Manila cell motility 40 0.0323887 595
Manila programmed cell death 40 0.0323887 600
Manila protein-containing complex assembly 39 0.0315789 444
Manila immune system process 36 0.0291498 670
Manila mitotic cell cycle 33 0.0267206 363
Manila vesicle-mediated transport 29 0.0234818 484
Manila cilium organization 28 0.0226721 178
Manila protein catabolic process 28 0.0226721 302
Manila nervous system process 27 0.0218623 358
Manila microtubule-based movement 25 0.0202429 161
Manila mRNA metabolic process 23 0.0186235 197
Manila transmembrane transport 21 0.0170040 330
Manila cell adhesion 18 0.0145749 387
Manila carbohydrate derivative metabolic process 17 0.0137652 301
Manila DNA repair 16 0.0129555 181
Manila cell junction organization 16 0.0129555 279
Manila membrane organization 15 0.0121457 278
Manila nucleobase-containing small molecule metabolic process 15 0.0121457 172
Manila lipid metabolic process 14 0.0113360 352
Manila autophagy 12 0.0097166 161
Manila chromosome segregation 12 0.0097166 140
Manila defense response to other organism 12 0.0097166 294
Manila generation of precursor metabolites and energy 11 0.0089069 105
Manila cytokinesis 10 0.0080972 96
Manila mitotic nuclear division 10 0.0080972 132
Manila chromatin organization 9 0.0072874 115
Manila establishment or maintenance of cell polarity 9 0.0072874 105
Manila intracellular protein transport 9 0.0072874 219
Manila DNA recombination 8 0.0064777 124
Manila DNA replication 8 0.0064777 102
Manila circulatory system process 8 0.0064777 189
Manila ribosome biogenesis 8 0.0064777 69
Manila carbohydrate metabolic process 7 0.0056680 159
Manila cellular amino acid metabolic process 7 0.0056680 88
Manila nucleocytoplasmic transport 7 0.0056680 108
Manila muscle system process 6 0.0048583 127
Manila protein localization to plasma membrane 6 0.0048583 68
Manila telomere organization 6 0.0048583 80
Manila gene silencing by RNA 5 0.0040486 34
Manila inflammatory response 5 0.0040486 135
Manila mitochondrion organization 5 0.0040486 168
Manila cellular modified amino acid metabolic process 4 0.0032389 76
Manila sulfur compound metabolic process 4 0.0032389 109
Manila tRNA metabolic process 4 0.0032389 40
Manila cytoplasmic translation 3 0.0024291 17
Manila meiotic nuclear division 3 0.0024291 79
Manila wound healing 3 0.0024291 97
Manila extracellular matrix organization 2 0.0016194 58
Manila protein folding 2 0.0016194 29
Manila protein maturation 2 0.0016194 107
Manila snRNA metabolic process 2 0.0016194 16
Manila NA 1 0.0008097 1
Manila detoxification 1 0.0008097 18
Manila lysosome organization 1 0.0008097 16
Manila nitrogen cycle metabolic process 1 0.0008097 6
Manila protein glycosylation 1 0.0008097 55
Manila renal system process 1 0.0008097 48
Manila respiratory system process 1 0.0008097 17
Manila_r anatomical structure development 149 0.1071942 1853
Manila_r signaling 126 0.0906475 1603
Manila_r cell differentiation 96 0.0690647 1281
Manila_r cytoskeleton organization 68 0.0489209 516
Manila_r DNA-templated transcription 60 0.0431655 741
Manila_r regulation of DNA-templated transcription 55 0.0395683 678
Manila_r reproductive process 55 0.0395683 536
Manila_r programmed cell death 44 0.0316547 600
Manila_r immune system process 42 0.0302158 670
Manila_r protein-containing complex assembly 42 0.0302158 444
Manila_r cell motility 41 0.0294964 595
Manila_r mitotic cell cycle 36 0.0258993 363
Manila_r vesicle-mediated transport 35 0.0251799 484
Manila_r nervous system process 32 0.0230216 358
Manila_r protein catabolic process 31 0.0223022 302
Manila_r cilium organization 30 0.0215827 178
Manila_r microtubule-based movement 27 0.0194245 161
Manila_r mRNA metabolic process 26 0.0187050 197
Manila_r transmembrane transport 25 0.0179856 330
Manila_r cell adhesion 21 0.0151079 387
Manila_r cell junction organization 20 0.0143885 279
Manila_r DNA repair 19 0.0136691 181
Manila_r carbohydrate derivative metabolic process 17 0.0122302 301
Manila_r lipid metabolic process 17 0.0122302 352
Manila_r membrane organization 17 0.0122302 278
Manila_r defense response to other organism 16 0.0115108 294
Manila_r nucleobase-containing small molecule metabolic process 15 0.0107914 172
Manila_r cytokinesis 13 0.0093525 96
Manila_r autophagy 12 0.0086331 161
Manila_r chromosome segregation 12 0.0086331 140
Manila_r generation of precursor metabolites and energy 12 0.0086331 105
Manila_r DNA replication 11 0.0079137 102
Manila_r chromatin organization 11 0.0079137 115
Manila_r circulatory system process 10 0.0071942 189
Manila_r establishment or maintenance of cell polarity 10 0.0071942 105
Manila_r intracellular protein transport 10 0.0071942 219
Manila_r DNA recombination 9 0.0064748 124
Manila_r cellular amino acid metabolic process 9 0.0064748 88
Manila_r mitotic nuclear division 9 0.0064748 132
Manila_r nucleocytoplasmic transport 8 0.0057554 108
Manila_r ribosome biogenesis 8 0.0057554 69
Manila_r carbohydrate metabolic process 7 0.0050360 159
Manila_r protein localization to plasma membrane 7 0.0050360 68
Manila_r gene silencing by RNA 6 0.0043165 34
Manila_r inflammatory response 6 0.0043165 135
Manila_r mitochondrion organization 6 0.0043165 168
Manila_r muscle system process 6 0.0043165 127
Manila_r telomere organization 6 0.0043165 80
Manila_r sulfur compound metabolic process 5 0.0035971 109
Manila_r cellular modified amino acid metabolic process 4 0.0028777 76
Manila_r cytoplasmic translation 4 0.0028777 17
Manila_r meiotic nuclear division 4 0.0028777 79
Manila_r tRNA metabolic process 4 0.0028777 40
Manila_r snRNA metabolic process 3 0.0021583 16
Manila_r wound healing 3 0.0021583 97
Manila_r extracellular matrix organization 2 0.0014388 58
Manila_r protein folding 2 0.0014388 29
Manila_r protein maturation 2 0.0014388 107
Manila_r NA 1 0.0007194 1
Manila_r detoxification 1 0.0007194 18
Manila_r lysosome organization 1 0.0007194 16
Manila_r nitrogen cycle metabolic process 1 0.0007194 6
Manila_r protein glycosylation 1 0.0007194 55
Manila_r renal system process 1 0.0007194 48
Manila_r respiratory system process 1 0.0007194 17
Mercenaria anatomical structure development 247 0.1123749 1853
Mercenaria signaling 189 0.0859873 1603
Mercenaria cell differentiation 170 0.0773430 1281
Mercenaria DNA-templated transcription 88 0.0400364 741
Mercenaria cytoskeleton organization 87 0.0395814 516
Mercenaria cell motility 83 0.0377616 595
Mercenaria regulation of DNA-templated transcription 82 0.0373066 678
Mercenaria reproductive process 71 0.0323021 536
Mercenaria immune system process 66 0.0300273 670
Mercenaria programmed cell death 63 0.0286624 600
Mercenaria vesicle-mediated transport 62 0.0282075 484
Mercenaria protein-containing complex assembly 58 0.0263876 444
Mercenaria nervous system process 48 0.0218380 358
Mercenaria mitotic cell cycle 47 0.0213831 363
Mercenaria cilium organization 46 0.0209281 178
Mercenaria cell adhesion 44 0.0200182 387
Mercenaria lipid metabolic process 40 0.0181984 352
Mercenaria protein catabolic process 39 0.0177434 302
Mercenaria carbohydrate derivative metabolic process 38 0.0172884 301
Mercenaria microtubule-based movement 37 0.0168335 161
Mercenaria cell junction organization 36 0.0163785 279
Mercenaria membrane organization 35 0.0159236 278
Mercenaria transmembrane transport 34 0.0154686 330
Mercenaria DNA repair 30 0.0136488 181
Mercenaria mRNA metabolic process 28 0.0127389 197
Mercenaria intracellular protein transport 24 0.0109190 219
Mercenaria defense response to other organism 23 0.0104641 294
Mercenaria carbohydrate metabolic process 22 0.0100091 159
Mercenaria nucleobase-containing small molecule metabolic process 22 0.0100091 172
Mercenaria circulatory system process 21 0.0095541 189
Mercenaria autophagy 20 0.0090992 161
Mercenaria cytokinesis 19 0.0086442 96
Mercenaria establishment or maintenance of cell polarity 17 0.0077343 105
Mercenaria chromatin organization 16 0.0072793 115
Mercenaria nucleocytoplasmic transport 16 0.0072793 108
Mercenaria DNA recombination 15 0.0068244 124
Mercenaria chromosome segregation 15 0.0068244 140
Mercenaria DNA replication 14 0.0063694 102
Mercenaria generation of precursor metabolites and energy 14 0.0063694 105
Mercenaria protein localization to plasma membrane 14 0.0063694 68
Mercenaria cellular amino acid metabolic process 11 0.0050045 88
Mercenaria mitochondrion organization 11 0.0050045 168
Mercenaria mitotic nuclear division 11 0.0050045 132
Mercenaria inflammatory response 10 0.0045496 135
Mercenaria sulfur compound metabolic process 10 0.0045496 109
Mercenaria protein maturation 9 0.0040946 107
Mercenaria tRNA metabolic process 9 0.0040946 40
Mercenaria muscle system process 8 0.0036397 127
Mercenaria telomere organization 8 0.0036397 80
Mercenaria cytoplasmic translation 6 0.0027298 17
Mercenaria extracellular matrix organization 6 0.0027298 58
Mercenaria protein glycosylation 6 0.0027298 55
Mercenaria cellular modified amino acid metabolic process 5 0.0022748 76
Mercenaria gene silencing by RNA 5 0.0022748 34
Mercenaria meiotic nuclear division 5 0.0022748 79
Mercenaria ribosome biogenesis 5 0.0022748 69
Mercenaria endocrine process 4 0.0018198 32
Mercenaria vitamin metabolic process 4 0.0018198 38
Mercenaria wound healing 4 0.0018198 97
Mercenaria lysosome organization 3 0.0013649 16
Mercenaria mitochondrial gene expression 3 0.0013649 25
Mercenaria nitrogen cycle metabolic process 3 0.0013649 6
Mercenaria detoxification 2 0.0009099 18
Mercenaria digestive system process 2 0.0009099 41
Mercenaria renal system process 2 0.0009099 48
Mercenaria respiratory system process 2 0.0009099 17
Mercenaria snRNA metabolic process 2 0.0009099 16
Mercenaria NA 1 0.0004550 1
Mercenaria peroxisome organization 1 0.0004550 15
Mercenaria_r anatomical structure development 768 0.1092927 1853
Mercenaria_r signaling 635 0.0903657 1603
Mercenaria_r cell differentiation 517 0.0735734 1281
Mercenaria_r DNA-templated transcription 267 0.0379963 741
Mercenaria_r regulation of DNA-templated transcription 245 0.0348655 678
Mercenaria_r cell motility 241 0.0342963 595
Mercenaria_r cytoskeleton organization 237 0.0337271 516
Mercenaria_r immune system process 232 0.0330155 670
Mercenaria_r programmed cell death 229 0.0325886 600
Mercenaria_r vesicle-mediated transport 218 0.0310232 484
Mercenaria_r reproductive process 202 0.0287463 536
Mercenaria_r protein-containing complex assembly 174 0.0247616 444
Mercenaria_r cell adhesion 163 0.0231962 387
Mercenaria_r nervous system process 153 0.0217732 358
Mercenaria_r lipid metabolic process 152 0.0216309 352
Mercenaria_r mitotic cell cycle 142 0.0202078 363
Mercenaria_r transmembrane transport 133 0.0189270 330
Mercenaria_r carbohydrate derivative metabolic process 131 0.0186424 301
Mercenaria_r membrane organization 118 0.0167924 278
Mercenaria_r cell junction organization 114 0.0162231 279
Mercenaria_r protein catabolic process 111 0.0157962 302
Mercenaria_r defense response to other organism 101 0.0143731 294
Mercenaria_r cilium organization 99 0.0140885 178
Mercenaria_r intracellular protein transport 85 0.0120962 219
Mercenaria_r DNA repair 82 0.0116693 181
Mercenaria_r mRNA metabolic process 81 0.0115270 197
Mercenaria_r carbohydrate metabolic process 77 0.0109577 159
Mercenaria_r microtubule-based movement 76 0.0108154 161
Mercenaria_r nucleobase-containing small molecule metabolic process 74 0.0105308 172
Mercenaria_r circulatory system process 70 0.0099616 189
Mercenaria_r autophagy 63 0.0089654 161
Mercenaria_r mitochondrion organization 60 0.0085385 168
Mercenaria_r chromosome segregation 53 0.0075423 140
Mercenaria_r DNA recombination 52 0.0074000 124
Mercenaria_r chromatin organization 48 0.0068308 115
Mercenaria_r generation of precursor metabolites and energy 46 0.0065462 105
Mercenaria_r DNA replication 45 0.0064039 102
Mercenaria_r nucleocytoplasmic transport 44 0.0062616 108
Mercenaria_r inflammatory response 43 0.0061193 135
Mercenaria_r mitotic nuclear division 43 0.0061193 132
Mercenaria_r cytokinesis 42 0.0059769 96
Mercenaria_r muscle system process 42 0.0059769 127
Mercenaria_r sulfur compound metabolic process 42 0.0059769 109
Mercenaria_r establishment or maintenance of cell polarity 41 0.0058346 105
Mercenaria_r protein localization to plasma membrane 41 0.0058346 68
Mercenaria_r cellular amino acid metabolic process 38 0.0054077 88
Mercenaria_r protein maturation 38 0.0054077 107
Mercenaria_r cellular modified amino acid metabolic process 30 0.0042692 76
Mercenaria_r meiotic nuclear division 30 0.0042692 79
Mercenaria_r wound healing 30 0.0042692 97
Mercenaria_r ribosome biogenesis 25 0.0035577 69
Mercenaria_r telomere organization 25 0.0035577 80
Mercenaria_r protein glycosylation 23 0.0032731 55
Mercenaria_r tRNA metabolic process 19 0.0027039 40
Mercenaria_r extracellular matrix organization 16 0.0022769 58
Mercenaria_r gene silencing by RNA 15 0.0021346 34
Mercenaria_r protein folding 15 0.0021346 29
Mercenaria_r cytoplasmic translation 12 0.0017077 17
Mercenaria_r endocrine process 12 0.0017077 32
Mercenaria_r vitamin metabolic process 12 0.0017077 38
Mercenaria_r renal system process 10 0.0014231 48
Mercenaria_r respiratory system process 8 0.0011385 17
Mercenaria_r lysosome organization 7 0.0009962 16
Mercenaria_r detoxification 6 0.0008538 18
Mercenaria_r digestive system process 6 0.0008538 41
Mercenaria_r mitochondrial gene expression 4 0.0005692 25
Mercenaria_r nitrogen cycle metabolic process 4 0.0005692 6
Mercenaria_r snRNA metabolic process 4 0.0005692 16
Mercenaria_r peroxisome organization 3 0.0004269 15
Mercenaria_r cell wall organization or biogenesis 2 0.0002846 13
Mercenaria_r NA 1 0.0001423 1

TISSUES

  • gonad
  • ctenidia
  • heart
  • juvenile
  • larvae
Total Terms per Tissue(s)
tissue total_n
ctenidia 15911
gonad 14715
heart 16021
juvenile 17277
larvae 16632
NA NA

Normalized Tissue Data

filtered_data <- tissue_goslims %>%
  filter(tissue %in% c("ctenidia", "heart", "gonad", "larvae", "juvenile")) %>%
  mutate(n_divided = case_when(tissue == "ctenidia" ~ n/15911,
                               tissue == "heart" ~ n/16021, 
                               tissue == "gonad" ~ n/14715, 
                               tissue == "larvae" ~ n/16632,
                               tissue == "juvenile" ~ n/17277)) 
kable(Tis_normal[1:7,])
tissue Term_unique n_tissue n_divided n_Pgen Pgen_normalized normalized log_scale
juvenile anatomical structure development 1817 0.1051687 1853 0.1052183 0.9995285 -0.0004716
larvae anatomical structure development 1743 0.1047980 1853 0.1052183 0.9960050 -0.0040030
heart anatomical structure development 1678 0.1047375 1853 0.1052183 0.9954305 -0.0045800
ctenidia anatomical structure development 1661 0.1043932 1853 0.1052183 0.9921578 -0.0078731
juvenile signaling 1572 0.0909880 1603 0.0910227 0.9996195 -0.0003806
gonad anatomical structure development 1524 0.1035678 1853 0.1052183 0.9843132 -0.0158112
larvae signaling 1501 0.0902477 1603 0.0910227 0.9914863 -0.0085502

Species Heatmap normalized by P. generosa transcriptopme where white = 0.9

Tissue Heatmap normalized by P. generosa transcriptome where white = 0.9