library(tidyverse)
## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr 1.1.4 ✔ readr 2.1.5
## ✔ forcats 1.0.0 ✔ stringr 1.5.1
## ✔ ggplot2 3.5.2 ✔ tibble 3.3.0
## ✔ lubridate 1.9.4 ✔ tidyr 1.3.1
## ✔ purrr 1.0.4
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
Phel <- read.delim("../output/18-annot-pycno/Phel_immune_shortlist.txt",
header = TRUE,
stringsAsFactors = FALSE)
head(Phel)
## transcript_id PSC.0519 PSC.0525 PSC.0531 PSC.0537 PSC.0549 PSC.0561 sum
## 1 g5770.t1 489 1524 191 502 98 998 3802
## 2 g5770.t1 489 1524 191 502 98 998 3802
## 3 g2184.t1 1337 1651 866 1370 517 1794 7535
## 4 g2184.t1 1337 1651 866 1370 517 1794 7535
## 5 g2184.t1 1337 1651 866 1370 517 1794 7535
## 6 g2184.t1 1337 1651 866 1370 517 1794 7535
## mean std.dev std.error Entry gene_name Entry.Name
## 1 633.6667 537.8828 219.5897 Q60636 PRDM1_MOUSE PRDM1_MOUSE
## 2 633.6667 537.8828 219.5897 Q60636 PRDM1_MOUSE PRDM1_MOUSE
## 3 1255.8333 482.3374 196.9134 Q9UGM3 DMBT1_HUMAN DMBT1_HUMAN
## 4 1255.8333 482.3374 196.9134 Q9UGM3 DMBT1_HUMAN DMBT1_HUMAN
## 5 1255.8333 482.3374 196.9134 Q9UGM3 DMBT1_HUMAN DMBT1_HUMAN
## 6 1255.8333 482.3374 196.9134 Q9UGM3 DMBT1_HUMAN DMBT1_HUMAN
## Protein.Names
## 1 PR domain zinc finger protein 1 (EC 2.1.1.-) (B lymphocyte-induced maturation protein 1) (Blimp-1) (Beta-interferon gene positive regulatory domain I-binding factor) (PR domain-containing protein 1)
## 2 PR domain zinc finger protein 1 (EC 2.1.1.-) (B lymphocyte-induced maturation protein 1) (Blimp-1) (Beta-interferon gene positive regulatory domain I-binding factor) (PR domain-containing protein 1)
## 3 Scavenger receptor cysteine-rich domain-containing protein DMBT1 (Deleted in malignant brain tumors 1 protein) (Glycoprotein 340) (Gp-340) (Hensin) (Salivary agglutinin) (SAG) (Surfactant pulmonary-associated D-binding protein)
## 4 Scavenger receptor cysteine-rich domain-containing protein DMBT1 (Deleted in malignant brain tumors 1 protein) (Glycoprotein 340) (Gp-340) (Hensin) (Salivary agglutinin) (SAG) (Surfactant pulmonary-associated D-binding protein)
## 5 Scavenger receptor cysteine-rich domain-containing protein DMBT1 (Deleted in malignant brain tumors 1 protein) (Glycoprotein 340) (Gp-340) (Hensin) (Salivary agglutinin) (SAG) (Surfactant pulmonary-associated D-binding protein)
## 6 Scavenger receptor cysteine-rich domain-containing protein DMBT1 (Deleted in malignant brain tumors 1 protein) (Glycoprotein 340) (Gp-340) (Hensin) (Salivary agglutinin) (SAG) (Surfactant pulmonary-associated D-binding protein)
## Gene.Names Organism
## 1 Prdm1 Blimp1 Mus musculus (Mouse)
## 2 Prdm1 Blimp1 Mus musculus (Mouse)
## 3 DMBT1 GP340 Homo sapiens (Human)
## 4 DMBT1 GP340 Homo sapiens (Human)
## 5 DMBT1 GP340 Homo sapiens (Human)
## 6 DMBT1 GP340 Homo sapiens (Human)
## Gene.Ontology.biological.process
## 1 adaptive immune response [GO:0002250]; aorta development [GO:0035904]; artery morphogenesis [GO:0048844]; cardiac septum development [GO:0003279]; cell fate commitment [GO:0045165]; coronary vasculature development [GO:0060976]; embryonic placenta development [GO:0001892]; eye photoreceptor cell development [GO:0042462]; gene expression [GO:0010467]; germ cell development [GO:0007281]; heart valve development [GO:0003170]; in utero embryonic development [GO:0001701]; innate immune response [GO:0045087]; intestinal epithelial cell development [GO:0060576]; kidney development [GO:0001822]; maternal placenta development [GO:0001893]; methylation [GO:0032259]; morphogenesis of a branching structure [GO:0001763]; negative regulation of B cell proliferation [GO:0030889]; negative regulation of gene expression [GO:0010629]; negative regulation of lipopolysaccharide-mediated signaling pathway [GO:0031665]; negative regulation of transcription by RNA polymerase II [GO:0000122]; positive regulation of B cell differentiation [GO:0045579]; positive regulation of gene expression [GO:0010628]; post-embryonic development [GO:0009791]; regulation of cell population proliferation [GO:0042127]; regulation of extrathymic T cell differentiation [GO:0033082]; regulation of natural killer cell differentiation [GO:0032823]; regulation of NK T cell differentiation [GO:0051136]; regulation of transcription by RNA polymerase II [GO:0006357]; retinal bipolar neuron differentiation [GO:0060040]; sebum secreting cell proliferation [GO:1990654]; trophoblast giant cell differentiation [GO:0060707]; ventricular septum development [GO:0003281]
## 2 adaptive immune response [GO:0002250]; aorta development [GO:0035904]; artery morphogenesis [GO:0048844]; cardiac septum development [GO:0003279]; cell fate commitment [GO:0045165]; coronary vasculature development [GO:0060976]; embryonic placenta development [GO:0001892]; eye photoreceptor cell development [GO:0042462]; gene expression [GO:0010467]; germ cell development [GO:0007281]; heart valve development [GO:0003170]; in utero embryonic development [GO:0001701]; innate immune response [GO:0045087]; intestinal epithelial cell development [GO:0060576]; kidney development [GO:0001822]; maternal placenta development [GO:0001893]; methylation [GO:0032259]; morphogenesis of a branching structure [GO:0001763]; negative regulation of B cell proliferation [GO:0030889]; negative regulation of gene expression [GO:0010629]; negative regulation of lipopolysaccharide-mediated signaling pathway [GO:0031665]; negative regulation of transcription by RNA polymerase II [GO:0000122]; positive regulation of B cell differentiation [GO:0045579]; positive regulation of gene expression [GO:0010628]; post-embryonic development [GO:0009791]; regulation of cell population proliferation [GO:0042127]; regulation of extrathymic T cell differentiation [GO:0033082]; regulation of natural killer cell differentiation [GO:0032823]; regulation of NK T cell differentiation [GO:0051136]; regulation of transcription by RNA polymerase II [GO:0006357]; retinal bipolar neuron differentiation [GO:0060040]; sebum secreting cell proliferation [GO:1990654]; trophoblast giant cell differentiation [GO:0060707]; ventricular septum development [GO:0003281]
## 3 defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 4 defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 5 defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 6 defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## Gene.Ontology.cellular.component
## 1 cytoplasm [GO:0005737]; nucleolus [GO:0005730]; nucleoplasm [GO:0005654]; nucleus [GO:0005634]
## 2 cytoplasm [GO:0005737]; nucleolus [GO:0005730]; nucleoplasm [GO:0005654]; nucleus [GO:0005634]
## 3 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]
## 4 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]
## 5 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]
## 6 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]
## Gene.Ontology.GO
## 1 cytoplasm [GO:0005737]; nucleolus [GO:0005730]; nucleoplasm [GO:0005654]; nucleus [GO:0005634]; DNA-binding transcription repressor activity, RNA polymerase II-specific [GO:0001227]; histone deacetylase binding [GO:0042826]; histone methyltransferase binding [GO:1990226]; methyltransferase activity [GO:0008168]; promoter-specific chromatin binding [GO:1990841]; RNA polymerase II cis-regulatory region sequence-specific DNA binding [GO:0000978]; sequence-specific DNA binding [GO:0043565]; transcription cis-regulatory region binding [GO:0000976]; zinc ion binding [GO:0008270]; adaptive immune response [GO:0002250]; aorta development [GO:0035904]; artery morphogenesis [GO:0048844]; cardiac septum development [GO:0003279]; cell fate commitment [GO:0045165]; coronary vasculature development [GO:0060976]; embryonic placenta development [GO:0001892]; eye photoreceptor cell development [GO:0042462]; gene expression [GO:0010467]; germ cell development [GO:0007281]; heart valve development [GO:0003170]; in utero embryonic development [GO:0001701]; innate immune response [GO:0045087]; intestinal epithelial cell development [GO:0060576]; kidney development [GO:0001822]; maternal placenta development [GO:0001893]; methylation [GO:0032259]; morphogenesis of a branching structure [GO:0001763]; negative regulation of B cell proliferation [GO:0030889]; negative regulation of gene expression [GO:0010629]; negative regulation of lipopolysaccharide-mediated signaling pathway [GO:0031665]; negative regulation of transcription by RNA polymerase II [GO:0000122]; positive regulation of B cell differentiation [GO:0045579]; positive regulation of gene expression [GO:0010628]; post-embryonic development [GO:0009791]; regulation of cell population proliferation [GO:0042127]; regulation of extrathymic T cell differentiation [GO:0033082]; regulation of natural killer cell differentiation [GO:0032823]; regulation of NK T cell differentiation [GO:0051136]; regulation of transcription by RNA polymerase II [GO:0006357]; retinal bipolar neuron differentiation [GO:0060040]; sebum secreting cell proliferation [GO:1990654]; trophoblast giant cell differentiation [GO:0060707]; ventricular septum development [GO:0003281]
## 2 cytoplasm [GO:0005737]; nucleolus [GO:0005730]; nucleoplasm [GO:0005654]; nucleus [GO:0005634]; DNA-binding transcription repressor activity, RNA polymerase II-specific [GO:0001227]; histone deacetylase binding [GO:0042826]; histone methyltransferase binding [GO:1990226]; methyltransferase activity [GO:0008168]; promoter-specific chromatin binding [GO:1990841]; RNA polymerase II cis-regulatory region sequence-specific DNA binding [GO:0000978]; sequence-specific DNA binding [GO:0043565]; transcription cis-regulatory region binding [GO:0000976]; zinc ion binding [GO:0008270]; adaptive immune response [GO:0002250]; aorta development [GO:0035904]; artery morphogenesis [GO:0048844]; cardiac septum development [GO:0003279]; cell fate commitment [GO:0045165]; coronary vasculature development [GO:0060976]; embryonic placenta development [GO:0001892]; eye photoreceptor cell development [GO:0042462]; gene expression [GO:0010467]; germ cell development [GO:0007281]; heart valve development [GO:0003170]; in utero embryonic development [GO:0001701]; innate immune response [GO:0045087]; intestinal epithelial cell development [GO:0060576]; kidney development [GO:0001822]; maternal placenta development [GO:0001893]; methylation [GO:0032259]; morphogenesis of a branching structure [GO:0001763]; negative regulation of B cell proliferation [GO:0030889]; negative regulation of gene expression [GO:0010629]; negative regulation of lipopolysaccharide-mediated signaling pathway [GO:0031665]; negative regulation of transcription by RNA polymerase II [GO:0000122]; positive regulation of B cell differentiation [GO:0045579]; positive regulation of gene expression [GO:0010628]; post-embryonic development [GO:0009791]; regulation of cell population proliferation [GO:0042127]; regulation of extrathymic T cell differentiation [GO:0033082]; regulation of natural killer cell differentiation [GO:0032823]; regulation of NK T cell differentiation [GO:0051136]; regulation of transcription by RNA polymerase II [GO:0006357]; retinal bipolar neuron differentiation [GO:0060040]; sebum secreting cell proliferation [GO:1990654]; trophoblast giant cell differentiation [GO:0060707]; ventricular septum development [GO:0003281]
## 3 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]; calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]; defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 4 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]; calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]; defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 5 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]; calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]; defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 6 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]; calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]; defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## Gene.Ontology.Molecular.Function
## 1 DNA-binding transcription repressor activity, RNA polymerase II-specific [GO:0001227]; histone deacetylase binding [GO:0042826]; histone methyltransferase binding [GO:1990226]; methyltransferase activity [GO:0008168]; promoter-specific chromatin binding [GO:1990841]; RNA polymerase II cis-regulatory region sequence-specific DNA binding [GO:0000978]; sequence-specific DNA binding [GO:0043565]; transcription cis-regulatory region binding [GO:0000976]; zinc ion binding [GO:0008270]
## 2 DNA-binding transcription repressor activity, RNA polymerase II-specific [GO:0001227]; histone deacetylase binding [GO:0042826]; histone methyltransferase binding [GO:1990226]; methyltransferase activity [GO:0008168]; promoter-specific chromatin binding [GO:1990841]; RNA polymerase II cis-regulatory region sequence-specific DNA binding [GO:0000978]; sequence-specific DNA binding [GO:0043565]; transcription cis-regulatory region binding [GO:0000976]; zinc ion binding [GO:0008270]
## 3 calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]
## 4 calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]
## 5 calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]
## 6 calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]
## Gene.Ontology.IDs
## 1 GO:0000122; GO:0000976; GO:0000978; GO:0001227; GO:0001701; GO:0001763; GO:0001822; GO:0001892; GO:0001893; GO:0002250; GO:0003170; GO:0003279; GO:0003281; GO:0005634; GO:0005654; GO:0005730; GO:0005737; GO:0006357; GO:0007281; GO:0008168; GO:0008270; GO:0009791; GO:0010467; GO:0010628; GO:0010629; GO:0030889; GO:0031665; GO:0032259; GO:0032823; GO:0033082; GO:0035904; GO:0042127; GO:0042462; GO:0042826; GO:0043565; GO:0045087; GO:0045165; GO:0045579; GO:0048844; GO:0051136; GO:0060040; GO:0060576; GO:0060707; GO:0060976; GO:1990226; GO:1990654; GO:1990841
## 2 GO:0000122; GO:0000976; GO:0000978; GO:0001227; GO:0001701; GO:0001763; GO:0001822; GO:0001892; GO:0001893; GO:0002250; GO:0003170; GO:0003279; GO:0003281; GO:0005634; GO:0005654; GO:0005730; GO:0005737; GO:0006357; GO:0007281; GO:0008168; GO:0008270; GO:0009791; GO:0010467; GO:0010628; GO:0010629; GO:0030889; GO:0031665; GO:0032259; GO:0032823; GO:0033082; GO:0035904; GO:0042127; GO:0042462; GO:0042826; GO:0043565; GO:0045087; GO:0045165; GO:0045579; GO:0048844; GO:0051136; GO:0060040; GO:0060576; GO:0060707; GO:0060976; GO:1990226; GO:1990654; GO:1990841
## 3 GO:0005044; GO:0005576; GO:0005615; GO:0005737; GO:0006952; GO:0015031; GO:0030670; GO:0030855; GO:0031012; GO:0035375; GO:0038187; GO:0042589; GO:0043152; GO:0045087; GO:0048306; GO:0050829; GO:0050830; GO:0051607; GO:0070062
## 4 GO:0005044; GO:0005576; GO:0005615; GO:0005737; GO:0006952; GO:0015031; GO:0030670; GO:0030855; GO:0031012; GO:0035375; GO:0038187; GO:0042589; GO:0043152; GO:0045087; GO:0048306; GO:0050829; GO:0050830; GO:0051607; GO:0070062
## 5 GO:0005044; GO:0005576; GO:0005615; GO:0005737; GO:0006952; GO:0015031; GO:0030670; GO:0030855; GO:0031012; GO:0035375; GO:0038187; GO:0042589; GO:0043152; GO:0045087; GO:0048306; GO:0050829; GO:0050830; GO:0051607; GO:0070062
## 6 GO:0005044; GO:0005576; GO:0005615; GO:0005737; GO:0006952; GO:0015031; GO:0030670; GO:0030855; GO:0031012; GO:0035375; GO:0038187; GO:0042589; GO:0043152; GO:0045087; GO:0048306; GO:0050829; GO:0050830; GO:0051607; GO:0070062
Pisa <- read.delim("../output/19-annot-pisaster/Pisaster_immune_shortlist.txt",
header = TRUE,
stringsAsFactors = FALSE)
head(Pisa)
## transcript_id PSC.0518 PSC.0524 PSC.0530 PSC.0536 PSC.0548 PSC.0560 sum
## 1 g15560.t1 1116 555 1294 1022 912 1424 6323
## 2 g6656.t1 248 123 671 343 346 532 2263
## 3 g12829.t1 15 97 13 0 39 15 179
## 4 g12829.t1 15 97 13 0 39 15 179
## 5 g12829.t1 15 97 13 0 39 15 179
## 6 g12829.t1 15 97 13 0 39 15 179
## mean std.dev std.error Entry gene_name
## 1 1053.83333 306.11528 124.97104 P55266 DSRAD_RAT
## 2 377.16667 196.84249 80.36061 E7F4Z4 ZDHC1_DANRE
## 3 29.83333 35.23871 14.38614 Q9UGM3 DMBT1_HUMAN
## 4 29.83333 35.23871 14.38614 Q9UGM3 DMBT1_HUMAN
## 5 29.83333 35.23871 14.38614 Q9UGM3 DMBT1_HUMAN
## 6 29.83333 35.23871 14.38614 Q9UGM3 DMBT1_HUMAN
## Protein.Names
## 1 Double-stranded RNA-specific adenosine deaminase (DRADA) (EC 3.5.4.37)
## 2 Palmitoyltransferase ZDHHC1 (EC 2.3.1.225) (DHHC domain-containing protein 1) (Zinc finger DHHC domain-containing protein 1)
## 3 Scavenger receptor cysteine-rich domain-containing protein DMBT1 (Deleted in malignant brain tumors 1 protein) (Glycoprotein 340) (Gp-340) (Hensin) (Salivary agglutinin) (SAG) (Surfactant pulmonary-associated D-binding protein)
## 4 Scavenger receptor cysteine-rich domain-containing protein DMBT1 (Deleted in malignant brain tumors 1 protein) (Glycoprotein 340) (Gp-340) (Hensin) (Salivary agglutinin) (SAG) (Surfactant pulmonary-associated D-binding protein)
## 5 Scavenger receptor cysteine-rich domain-containing protein DMBT1 (Deleted in malignant brain tumors 1 protein) (Glycoprotein 340) (Gp-340) (Hensin) (Salivary agglutinin) (SAG) (Surfactant pulmonary-associated D-binding protein)
## 6 Scavenger receptor cysteine-rich domain-containing protein DMBT1 (Deleted in malignant brain tumors 1 protein) (Glycoprotein 340) (Gp-340) (Hensin) (Salivary agglutinin) (SAG) (Surfactant pulmonary-associated D-binding protein)
## Gene.Names Organism
## 1 Adar Dsrad Rattus norvegicus (Rat)
## 2 zdhhc1 dhhc1 Danio rerio (Zebrafish) (Brachydanio rerio)
## 3 DMBT1 GP340 Homo sapiens (Human)
## 4 DMBT1 GP340 Homo sapiens (Human)
## 5 DMBT1 GP340 Homo sapiens (Human)
## 6 DMBT1 GP340 Homo sapiens (Human)
## Gene.Ontology.biological.process
## 1 adenosine to inosine editing [GO:0006382]; apoptotic process [GO:0006915]; base conversion or substitution editing [GO:0016553]; cellular response to virus [GO:0098586]; defense response to virus [GO:0051607]; definitive hemopoiesis [GO:0060216]; erythrocyte differentiation [GO:0030218]; hematopoietic progenitor cell differentiation [GO:0002244]; hematopoietic stem cell homeostasis [GO:0061484]; hepatocyte apoptotic process [GO:0097284]; innate immune response [GO:0045087]; miRNA processing [GO:0035196]; mRNA processing [GO:0006397]; negative regulation of hepatocyte apoptotic process [GO:1903944]; negative regulation of post-transcriptional gene silencing by regulatory ncRNA [GO:1900369]; negative regulation of protein kinase activity by regulation of protein phosphorylation [GO:0044387]; negative regulation of type I interferon-mediated signaling pathway [GO:0060339]; osteoblast differentiation [GO:0001649]; positive regulation of viral genome replication [GO:0045070]; pre-miRNA processing [GO:0031054]; response to interferon-alpha [GO:0035455]; response to virus [GO:0009615]; RISC complex assembly [GO:0070922]; RNA processing [GO:0006396]; somatic diversification of immune receptors via somatic mutation [GO:0002566]
## 2 antiviral innate immune response [GO:0140374]; positive regulation of NLRP3 inflammasome complex assembly [GO:1900227]; protein targeting to membrane [GO:0006612]
## 3 defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 4 defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 5 defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 6 defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## Gene.Ontology.cellular.component
## 1 cytoplasm [GO:0005737]; nuclear speck [GO:0016607]; nucleolus [GO:0005730]; nucleus [GO:0005634]; supraspliceosomal complex [GO:0044530]
## 2 endoplasmic reticulum [GO:0005783]; endoplasmic reticulum membrane [GO:0005789]; endosome membrane [GO:0010008]; Golgi apparatus [GO:0005794]
## 3 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]
## 4 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]
## 5 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]
## 6 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]
## Gene.Ontology.GO
## 1 cytoplasm [GO:0005737]; nuclear speck [GO:0016607]; nucleolus [GO:0005730]; nucleus [GO:0005634]; supraspliceosomal complex [GO:0044530]; DNA binding [GO:0003677]; double-stranded RNA adenosine deaminase activity [GO:0003726]; double-stranded RNA binding [GO:0003725]; metal ion binding [GO:0046872]; tRNA-specific adenosine deaminase activity [GO:0008251]; adenosine to inosine editing [GO:0006382]; apoptotic process [GO:0006915]; base conversion or substitution editing [GO:0016553]; cellular response to virus [GO:0098586]; defense response to virus [GO:0051607]; definitive hemopoiesis [GO:0060216]; erythrocyte differentiation [GO:0030218]; hematopoietic progenitor cell differentiation [GO:0002244]; hematopoietic stem cell homeostasis [GO:0061484]; hepatocyte apoptotic process [GO:0097284]; innate immune response [GO:0045087]; miRNA processing [GO:0035196]; mRNA processing [GO:0006397]; negative regulation of hepatocyte apoptotic process [GO:1903944]; negative regulation of post-transcriptional gene silencing by regulatory ncRNA [GO:1900369]; negative regulation of protein kinase activity by regulation of protein phosphorylation [GO:0044387]; negative regulation of type I interferon-mediated signaling pathway [GO:0060339]; osteoblast differentiation [GO:0001649]; positive regulation of viral genome replication [GO:0045070]; pre-miRNA processing [GO:0031054]; response to interferon-alpha [GO:0035455]; response to virus [GO:0009615]; RISC complex assembly [GO:0070922]; RNA processing [GO:0006396]; somatic diversification of immune receptors via somatic mutation [GO:0002566]
## 2 endoplasmic reticulum [GO:0005783]; endoplasmic reticulum membrane [GO:0005789]; endosome membrane [GO:0010008]; Golgi apparatus [GO:0005794]; protein-cysteine S-palmitoyltransferase activity [GO:0019706]; antiviral innate immune response [GO:0140374]; positive regulation of NLRP3 inflammasome complex assembly [GO:1900227]; protein targeting to membrane [GO:0006612]
## 3 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]; calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]; defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 4 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]; calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]; defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 5 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]; calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]; defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 6 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]; calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]; defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## Gene.Ontology.Molecular.Function
## 1 DNA binding [GO:0003677]; double-stranded RNA adenosine deaminase activity [GO:0003726]; double-stranded RNA binding [GO:0003725]; metal ion binding [GO:0046872]; tRNA-specific adenosine deaminase activity [GO:0008251]
## 2 protein-cysteine S-palmitoyltransferase activity [GO:0019706]
## 3 calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]
## 4 calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]
## 5 calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]
## 6 calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]
## Gene.Ontology.IDs
## 1 GO:0001649; GO:0002244; GO:0002566; GO:0003677; GO:0003725; GO:0003726; GO:0005634; GO:0005730; GO:0005737; GO:0006382; GO:0006396; GO:0006397; GO:0006915; GO:0008251; GO:0009615; GO:0016553; GO:0016607; GO:0030218; GO:0031054; GO:0035196; GO:0035455; GO:0044387; GO:0044530; GO:0045070; GO:0045087; GO:0046872; GO:0051607; GO:0060216; GO:0060339; GO:0061484; GO:0070922; GO:0097284; GO:0098586; GO:1900369; GO:1903944
## 2 GO:0005783; GO:0005789; GO:0005794; GO:0006612; GO:0010008; GO:0019706; GO:0140374; GO:1900227
## 3 GO:0005044; GO:0005576; GO:0005615; GO:0005737; GO:0006952; GO:0015031; GO:0030670; GO:0030855; GO:0031012; GO:0035375; GO:0038187; GO:0042589; GO:0043152; GO:0045087; GO:0048306; GO:0050829; GO:0050830; GO:0051607; GO:0070062
## 4 GO:0005044; GO:0005576; GO:0005615; GO:0005737; GO:0006952; GO:0015031; GO:0030670; GO:0030855; GO:0031012; GO:0035375; GO:0038187; GO:0042589; GO:0043152; GO:0045087; GO:0048306; GO:0050829; GO:0050830; GO:0051607; GO:0070062
## 5 GO:0005044; GO:0005576; GO:0005615; GO:0005737; GO:0006952; GO:0015031; GO:0030670; GO:0030855; GO:0031012; GO:0035375; GO:0038187; GO:0042589; GO:0043152; GO:0045087; GO:0048306; GO:0050829; GO:0050830; GO:0051607; GO:0070062
## 6 GO:0005044; GO:0005576; GO:0005615; GO:0005737; GO:0006952; GO:0015031; GO:0030670; GO:0030855; GO:0031012; GO:0035375; GO:0038187; GO:0042589; GO:0043152; GO:0045087; GO:0048306; GO:0050829; GO:0050830; GO:0051607; GO:0070062
Derm <- read.delim("../output/20-annot-derm/Derm_immune_shortlist.txt",
header = TRUE,
stringsAsFactors = FALSE)
head(Derm)
## transcript_id PSC.0523 PSC.0529 PSC.0529.1 PSC.0535 PSC.0547 PSC.0559 sum
## 1 g9822.t1 96 146 146 1002 885 0 2275
## 2 g9822.t1 96 146 146 1002 885 0 2275
## 3 g9822.t1 96 146 146 1002 885 0 2275
## 4 g9822.t1 96 146 146 1002 885 0 2275
## 5 g9822.t1 96 146 146 1002 885 0 2275
## 6 g9822.t1 96 146 146 1002 885 0 2275
## mean std.dev std.error Entry gene_name Entry.Name
## 1 379.1667 441.9214 180.4137 Q9UGM3 DMBT1_HUMAN DMBT1_HUMAN
## 2 379.1667 441.9214 180.4137 Q9UGM3 DMBT1_HUMAN DMBT1_HUMAN
## 3 379.1667 441.9214 180.4137 Q9UGM3 DMBT1_HUMAN DMBT1_HUMAN
## 4 379.1667 441.9214 180.4137 Q9UGM3 DMBT1_HUMAN DMBT1_HUMAN
## 5 379.1667 441.9214 180.4137 Q9UGM3 DMBT1_HUMAN DMBT1_HUMAN
## 6 379.1667 441.9214 180.4137 Q9UGM3 DMBT1_HUMAN DMBT1_HUMAN
## Protein.Names
## 1 Scavenger receptor cysteine-rich domain-containing protein DMBT1 (Deleted in malignant brain tumors 1 protein) (Glycoprotein 340) (Gp-340) (Hensin) (Salivary agglutinin) (SAG) (Surfactant pulmonary-associated D-binding protein)
## 2 Scavenger receptor cysteine-rich domain-containing protein DMBT1 (Deleted in malignant brain tumors 1 protein) (Glycoprotein 340) (Gp-340) (Hensin) (Salivary agglutinin) (SAG) (Surfactant pulmonary-associated D-binding protein)
## 3 Scavenger receptor cysteine-rich domain-containing protein DMBT1 (Deleted in malignant brain tumors 1 protein) (Glycoprotein 340) (Gp-340) (Hensin) (Salivary agglutinin) (SAG) (Surfactant pulmonary-associated D-binding protein)
## 4 Scavenger receptor cysteine-rich domain-containing protein DMBT1 (Deleted in malignant brain tumors 1 protein) (Glycoprotein 340) (Gp-340) (Hensin) (Salivary agglutinin) (SAG) (Surfactant pulmonary-associated D-binding protein)
## 5 Scavenger receptor cysteine-rich domain-containing protein DMBT1 (Deleted in malignant brain tumors 1 protein) (Glycoprotein 340) (Gp-340) (Hensin) (Salivary agglutinin) (SAG) (Surfactant pulmonary-associated D-binding protein)
## 6 Scavenger receptor cysteine-rich domain-containing protein DMBT1 (Deleted in malignant brain tumors 1 protein) (Glycoprotein 340) (Gp-340) (Hensin) (Salivary agglutinin) (SAG) (Surfactant pulmonary-associated D-binding protein)
## Gene.Names Organism
## 1 DMBT1 GP340 Homo sapiens (Human)
## 2 DMBT1 GP340 Homo sapiens (Human)
## 3 DMBT1 GP340 Homo sapiens (Human)
## 4 DMBT1 GP340 Homo sapiens (Human)
## 5 DMBT1 GP340 Homo sapiens (Human)
## 6 DMBT1 GP340 Homo sapiens (Human)
## Gene.Ontology.biological.process
## 1 defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 2 defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 3 defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 4 defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 5 defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 6 defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## Gene.Ontology.cellular.component
## 1 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]
## 2 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]
## 3 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]
## 4 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]
## 5 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]
## 6 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]
## Gene.Ontology.GO
## 1 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]; calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]; defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 2 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]; calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]; defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 3 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]; calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]; defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 4 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]; calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]; defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 5 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]; calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]; defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## 6 cytoplasm [GO:0005737]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; phagocytic vesicle membrane [GO:0030670]; zymogen granule membrane [GO:0042589]; calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]; defense response [GO:0006952]; defense response to Gram-negative bacterium [GO:0050829]; defense response to Gram-positive bacterium [GO:0050830]; defense response to virus [GO:0051607]; epithelial cell differentiation [GO:0030855]; induction of bacterial agglutination [GO:0043152]; innate immune response [GO:0045087]; protein transport [GO:0015031]
## Gene.Ontology.Molecular.Function
## 1 calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]
## 2 calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]
## 3 calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]
## 4 calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]
## 5 calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]
## 6 calcium-dependent protein binding [GO:0048306]; pattern recognition receptor activity [GO:0038187]; scavenger receptor activity [GO:0005044]; zymogen binding [GO:0035375]
## Gene.Ontology.IDs
## 1 GO:0005044; GO:0005576; GO:0005615; GO:0005737; GO:0006952; GO:0015031; GO:0030670; GO:0030855; GO:0031012; GO:0035375; GO:0038187; GO:0042589; GO:0043152; GO:0045087; GO:0048306; GO:0050829; GO:0050830; GO:0051607; GO:0070062
## 2 GO:0005044; GO:0005576; GO:0005615; GO:0005737; GO:0006952; GO:0015031; GO:0030670; GO:0030855; GO:0031012; GO:0035375; GO:0038187; GO:0042589; GO:0043152; GO:0045087; GO:0048306; GO:0050829; GO:0050830; GO:0051607; GO:0070062
## 3 GO:0005044; GO:0005576; GO:0005615; GO:0005737; GO:0006952; GO:0015031; GO:0030670; GO:0030855; GO:0031012; GO:0035375; GO:0038187; GO:0042589; GO:0043152; GO:0045087; GO:0048306; GO:0050829; GO:0050830; GO:0051607; GO:0070062
## 4 GO:0005044; GO:0005576; GO:0005615; GO:0005737; GO:0006952; GO:0015031; GO:0030670; GO:0030855; GO:0031012; GO:0035375; GO:0038187; GO:0042589; GO:0043152; GO:0045087; GO:0048306; GO:0050829; GO:0050830; GO:0051607; GO:0070062
## 5 GO:0005044; GO:0005576; GO:0005615; GO:0005737; GO:0006952; GO:0015031; GO:0030670; GO:0030855; GO:0031012; GO:0035375; GO:0038187; GO:0042589; GO:0043152; GO:0045087; GO:0048306; GO:0050829; GO:0050830; GO:0051607; GO:0070062
## 6 GO:0005044; GO:0005576; GO:0005615; GO:0005737; GO:0006952; GO:0015031; GO:0030670; GO:0030855; GO:0031012; GO:0035375; GO:0038187; GO:0042589; GO:0043152; GO:0045087; GO:0048306; GO:0050829; GO:0050830; GO:0051607; GO:0070062
Derm_unique <- Derm[!duplicated(Derm), ] %>% distinct(Entry, .keep_all = TRUE)
Phel_unique <- Phel[!duplicated(Phel), ] %>% distinct(Entry, .keep_all = TRUE)
Pisa_unique <- Pisa[!duplicated(Pisa), ] %>% distinct(Entry, .keep_all = TRUE)
joined_immune <- Derm_unique %>%
inner_join(Phel_unique, by = "Entry") %>%
inner_join(Pisa_unique, by = "Entry")
for (name in colnames(joined_immune)) {
cat(name, "\n")
}
## transcript_id.x
## PSC.0523
## PSC.0529
## PSC.0529.1
## PSC.0535
## PSC.0547
## PSC.0559
## sum.x
## mean.x
## std.dev.x
## std.error.x
## Entry
## gene_name.x
## Entry.Name.x
## Protein.Names.x
## Gene.Names.x
## Organism.x
## Gene.Ontology.biological.process.x
## Gene.Ontology.cellular.component.x
## Gene.Ontology.GO.x
## Gene.Ontology.Molecular.Function.x
## Gene.Ontology.IDs.x
## transcript_id.y
## PSC.0519
## PSC.0525
## PSC.0531
## PSC.0537
## PSC.0549
## PSC.0561
## sum.y
## mean.y
## std.dev.y
## std.error.y
## gene_name.y
## Entry.Name.y
## Protein.Names.y
## Gene.Names.y
## Organism.y
## Gene.Ontology.biological.process.y
## Gene.Ontology.cellular.component.y
## Gene.Ontology.GO.y
## Gene.Ontology.Molecular.Function.y
## Gene.Ontology.IDs.y
## transcript_id
## PSC.0518
## PSC.0524
## PSC.0530
## PSC.0536
## PSC.0548
## PSC.0560
## sum
## mean
## std.dev
## std.error
## gene_name
## Protein.Names
## Gene.Names
## Organism
## Gene.Ontology.biological.process
## Gene.Ontology.cellular.component
## Gene.Ontology.GO
## Gene.Ontology.Molecular.Function
## Gene.Ontology.IDs
selected_df <- joined_immune %>%
select(
Entry,
gene_name.x,
Entry.Name.x,
Protein.Names.x,
Gene.Names.x,
Gene.Ontology.biological.process.x,
transcript_id.x,
sum.x,
mean.x,
std.dev.x,
std.error.x,
transcript_id.y,
sum.y,
mean.y,
std.dev.y,
std.error.y,
transcript_id,
sum,
mean,
std.dev,
std.error
)
selected_df <- joined_immune %>%
select(
Entry,
gene_name.x,
Entry.Name.x,
Protein.Names.x,
Gene.Names.x,
Gene.Ontology.biological.process.x,
starts_with("transcript_id.x"),
starts_with("sum.x"),
starts_with("mean.x"),
starts_with("std.dev.x"),
starts_with("std.error.x"),
starts_with("transcript_id.y"),
starts_with("sum.y"),
starts_with("mean.y"),
starts_with("std.dev.y"),
starts_with("std.error.y"),
transcript_id,
sum,
mean,
std.dev,
std.error
) %>%
rename_with(~ gsub("\\.x$", "_Derm", .x), ends_with(".x")) %>%
rename_with(~ gsub("\\.y$", "_Phel", .x), ends_with(".y")) %>%
rename_with(~ paste0(.x, "_Pisa"), c("transcript_id", "sum", "mean", "std.dev", "std.error"))
selected_df <- selected_df %>%
rowwise() %>%
mutate(
mean_range = max(c_across(c(mean_Derm, mean_Phel, mean_Pisa))) -
min(c_across(c(mean_Derm, mean_Phel, mean_Pisa)))
) %>%
ungroup()
most_equal <- selected_df %>%
arrange(mean_range) %>%
slice(1:20) # Top 20 most similar
most_divergent <- selected_df %>%
arrange(desc(mean_range)) %>%
slice(1:20) # Top 20 most divergent