library(dplyr)##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, unionlibrary(tidyr)Perform functional annotation for miRNA-mRNA, lncRNA-mRNA, lncRNA-miRNA, etc. putative interactions.
The reference genome was annotated using Uniprot/Swissprot in deep-dive-expression/D-Apul/code/02-Apul-reference-annotation.
Load in reference annotations mapping
genome_IDmapping <- read.table("../output/02-Apul-reference-annotation/Apulcra-genome-mRNA-IDmapping-2024_12_12.tab", header=TRUE)# Read in RNAhybrid results for miRNAs that bind in the 3'UTR region of an mRNA
RNAhybrid_3UTR <- read.table("../output/16-Apul-RNAhybrid/Apul-RNAhybrid-mRNA-compact_3utr_worm-formatted.txt", sep="\t", header=TRUE)
# Filter to only retain highly likely hybridizations
RNAhybrid_3UTR_p0.01 <- RNAhybrid_3UTR %>%
filter(pval < 0.01)
# join with ID mapping to annotate
RNAhybrid_3UTR_p0.01_FA <- left_join(RNAhybrid_3UTR_p0.01, genome_IDmapping, by = c("target_name" = "V3"))# read in data
miRanda_pcor <- read.csv("../output/09-Apul-mRNA-miRNA-interactions/PCC_miRNA_mRNA.csv")
# read in FUN id - mRNA association table
mRNA_FUN_table <- read.table("../output/15-Apul-annotate-UTRs/Apul-mRNA-FUNids.txt")
# Remove "Parent=" prefix of the FUN IDs
mRNA_FUN_table$V4 <- gsub("Parent=", "", mRNA_FUN_table$V4)
# read in functional annotation mapping table and ensure unique rows
annot_tab <- read.table("../output/02-Apul-reference-annotation/Apulcra-genome-mRNA-IDmapping-2024_12_12.tab", header=TRUE) %>%
distinct(V1, .keep_all = TRUE)# Use FUN ids to annotate with associated mRNA coordinates
miRanda_pcor_annot <- left_join(miRanda_pcor, mRNA_FUN_table, by = c("mRNA" = "V4")) %>%
select(-V2, -V3, -V5)
# Use these mRNA coordinates to map to functional annotations
miRanda_pcor_annot <- left_join(miRanda_pcor_annot, annot_tab, by = c("V1" = "V1"))# Read in the data
miRanda_miRNA_mRNA <- read.table("../data/09-Apul-mRNA-miRNA-interactions/miranda_strict_all_1kb_parsed_apul_updated.txt")
colnames(miRanda_miRNA_mRNA) <- c("mirna", "target", "score", "energy", "miRNA_start", "miRNA_end", "target_start", "target_end", "aln_length", "subject_identity", "Qquery_identity")
# Separate the miRNA cluster names and locations
miRanda_miRNA_mRNA <- miRanda_miRNA_mRNA %>% separate(mirna, into = c("miRNA_cluster", "miRNA_location"), sep = "::")
miRanda_miRNA_mRNA$miRNA_cluster <- gsub("^>", "", miRanda_miRNA_mRNA$miRNA_cluster) # Remove leading >
miRanda_miRNA_mRNA$miRNA_cluster <- gsub("\\.mature$", "", miRanda_miRNA_mRNA$miRNA_cluster) # Remove trailing .mature
# Separate the mRNA FUN ids and locations
miRanda_miRNA_mRNA <- miRanda_miRNA_mRNA %>% separate(target, into = c("mRNA_FUNid", "mRNA_location"), sep = "::")
# Check
head(miRanda_miRNA_mRNA)## miRNA_cluster miRNA_location mRNA_FUNid
## 1 Cluster_10051 ptg000016l:7795530-7795551(+) FUN_000580
## 2 Cluster_10051 ptg000016l:7795530-7795551(+) FUN_000640
## 3 Cluster_10051 ptg000016l:7795530-7795551(+) FUN_001049
## 4 Cluster_10051 ptg000016l:7795530-7795551(+) FUN_001564
## 5 Cluster_10051 ptg000016l:7795530-7795551(+) FUN_002479
## 6 Cluster_10051 ptg000016l:7795530-7795551(+) FUN_002556
## mRNA_location score energy miRNA_start miRNA_end target_start
## 1 ntLink_6:4580655-4581655 162 -20.38 2 21 11
## 2 ntLink_6:5278186-5279186 156 -20.16 2 17 132
## 3 ntLink_6:7885174-7886174 169 -23.61 2 20 195
## 4 ntLink_6:13794539-13795539 163 -21.78 2 16 237
## 5 ntLink_8:2255969-2256969 166 -24.91 2 21 413
## 6 ntLink_8:3610299-3611299 159 -22.63 2 21 537
## target_end aln_length subject_identity Qquery_identity
## 1 31 19 73.68% 84.21%
## 2 153 15 73.33% 86.67%
## 3 218 20 80.00% 90.00%
## 4 258 14 85.71% 92.86%
## 5 433 19 73.68% 89.47%
## 6 559 20 65.00% 85.00%write.table(miRanda_miRNA_mRNA, "../output/18-Apul-interactions-functional-annotation/miRanda_miRNA_mRNA.txt", col.names = TRUE, row.names = FALSE,sep = "\t")# Read in the data
RNAhybrid_miRNA_mRNA <- read.table("../output/16-Apul-RNAhybrid/Apul-RNAhybrid-3UTR-compact_3utr_worm-formatted.txt", sep="\t", header=TRUE)
# Separate the miRNA cluster names and locations
RNAhybrid_miRNA_mRNA <- RNAhybrid_miRNA_mRNA %>% separate(query_name, into = c("miRNA_cluster", "miRNA_location"), sep = "::")
RNAhybrid_miRNA_mRNA$miRNA_cluster <- gsub("\\.mature$", "", RNAhybrid_miRNA_mRNA$miRNA_cluster) # Remove trailing .mature
write.table(RNAhybrid_miRNA_mRNA, "../output/18-Apul-interactions-functional-annotation/RNAhybrid_miRNA_mRNA.txt", col.names = TRUE, row.names = FALSE,sep = "\t")Both miRanda and RNAhybrid were run using 3’UTR regions as the target. Since there may be some formattign differences in identifying the 3UTr regions, I don’t think a left_join will work, because the target regions won’t match exactly.
Instead, maybe I can use bedtools intersect? Intersect will identify regions where both the miRanda and RNAhybrid outputs show a target-miRNA hybridization
Actually first, let’s try to look at the two in IGV
Make IGV inputs (super basic gff)
# Format miRanda for IGV as a gff
#!/bin/bash
# Input and output file paths
INPUT_FILE="../output/18-Apul-interactions-functional-annotation/miRanda_miRNA_mRNA.txt" # Replace with the path to your input file
OUTPUT_FILE="../output/18-Apul-interactions-functional-annotation/miranda_strict_all_1kb_parsed_apul_updated.gff"
# Write GFF3 header to the output file
echo "##gff-version 3" > "$OUTPUT_FILE"
# Process the input file, skipping the header line
tail -n +2 "$INPUT_FILE" | while IFS=$'\t' read -r miRNA_cluster miRNA_location mRNA_FUNid mRNA_location score energy miRNA_start miRNA_end target_start target_end aln_length subject_identity Qquery_identity
do
# Extract locus name and coordinates from target_name
locus=$(echo "$mRNA_location" | cut -d'"' -f2 | cut -d':' -f1)
start_coord=$(echo "$mRNA_location" | cut -d':' -f2 | cut -d'-' -f1)
start_gff=$((start_coord + target_start))
end_gff=$((start_gff + aln_length))
# Extract strandedness from query_name
strand=$(echo "$miRNA_location" | grep -o '(-\|+)' | tr -d '()')
# Write the GFF3 line
echo -e "$locus\tRNAhybrid\tmiRNA_binding\t$start_gff\t$end_gff\t.\t$strand\t.\tID=$miRNA_cluster;energy=$energy;score=$score" >> "$OUTPUT_FILE"
done
/home/shared/bedtools2/bin/bedtools intersect \
-a ../output/18-Apul-interactions-functional-annotation/miranda_strict_all_1kb_parsed_apul_updated.gff \
-b ../output/16-Apul-RNAhybrid/Apul-RNAhybrid-3UTR-compact_3utr_worm.gff \
-wa
/home/shared/bedtools2/bin/bedtools intersect \
-a ../output/16-Apul-RNAhybrid/Apul-RNAhybrid-3UTR-compact_3utr_worm.gff \
-b ../output/18-Apul-interactions-functional-annotation/miranda_strict_all_1kb_parsed_apul_updated.gff \
-wa## ptg000019l RNAhybrid miRNA_binding 3905988 3906006 . + . ID="Cluster_10051";energy=-20.49;score=157
## ptg000039l RNAhybrid miRNA_binding 1038025 1038045 . + . ID="Cluster_10051";energy=-27.39;score=167
## ntLink_8 RNAhybrid miRNA_binding 17362798 17362810 . - . ID="Cluster_10057";energy=-25.09;score=161
## ntLink_8 RNAhybrid miRNA_binding 17362798 17362810 . - . ID="Cluster_10057";energy=-25.09;score=161
## ntLink_8 RNAhybrid miRNA_binding 31354508 31354525 . - . ID="Cluster_10057";energy=-23.81;score=168
## ptg000002l RNAhybrid miRNA_binding 3411163 3411182 . - . ID="Cluster_10057";energy=-23.78;score=166
## ptg000008l RNAhybrid miRNA_binding 6343721 6343733 . - . ID="Cluster_10057";energy=-26.72;score=161
## ptg000011l RNAhybrid miRNA_binding 11819542 11819559 . - . ID="Cluster_10057";energy=-23.81;score=168
## ptg000015l RNAhybrid miRNA_binding 2404071 2404083 . - . ID="Cluster_10057";energy=-25.78;score=165
## ptg000015l RNAhybrid miRNA_binding 2404071 2404083 . - . ID="Cluster_10057";energy=-25.78;score=165
## ptg000020l RNAhybrid miRNA_binding 16091584 16091603 . - . ID="Cluster_10057";energy=-21.48;score=156
## ptg000020l RNAhybrid miRNA_binding 16493595 16493614 . - . ID="Cluster_10057";energy=-24.36;score=152
## ptg000023l RNAhybrid miRNA_binding 24634237 24634258 . - . ID="Cluster_10057";energy=-21.92;score=163
## ptg000025l RNAhybrid miRNA_binding 1210277 1210296 . - . ID="Cluster_10057";energy=-21.68;score=152
## ptg000026l RNAhybrid miRNA_binding 556244 556256 . - . ID="Cluster_10057";energy=-26.71;score=165
## ptg000026l RNAhybrid miRNA_binding 556244 556256 . - . ID="Cluster_10057";energy=-26.71;score=165
## ptg000026l RNAhybrid miRNA_binding 896120 896132 . - . ID="Cluster_10057";energy=-26.71;score=165
## ptg000026l RNAhybrid miRNA_binding 896120 896132 . - . ID="Cluster_10057";energy=-26.71;score=165
## ptg000036l RNAhybrid miRNA_binding 859237 859254 . - . ID="Cluster_10057";energy=-24.85;score=163
## ptg000047l RNAhybrid miRNA_binding 2819153 2819168 . - . ID="Cluster_10093";energy=-26.08;score=168
## ptg000047l RNAhybrid miRNA_binding 2819153 2819168 . - . ID="Cluster_10093";energy=-26.08;score=168
## ptg000047l RNAhybrid miRNA_binding 2819153 2819168 . - . ID="Cluster_10093";energy=-26.08;score=168
## ptg000047l RNAhybrid miRNA_binding 2819153 2819168 . - . ID="Cluster_10093";energy=-26.08;score=168
## ptg000021l RNAhybrid miRNA_binding 13553488 13553506 . + . ID="Cluster_14768";energy=-39.74;score=191
## ntLink_6 RNAhybrid miRNA_binding 15902887 15902912 . + . ID="Cluster_15316";energy=-24.16;score=155
## ptg000034l RNAhybrid miRNA_binding 183625 183643 . + . ID="Cluster_15316";energy=-27.08;score=179
## ptg000064l RNAhybrid miRNA_binding 99588 99606 . + . ID="Cluster_15316";energy=-27.08;score=179
## ptg000009l RNAhybrid miRNA_binding 10224585 10224598 . - . ID="Cluster_15340";energy=-22.98;score=170
## ptg000025l RNAhybrid miRNA_binding 5797264 5797281 . - . ID="Cluster_15340";energy=-30.09;score=182
## ptg000025l RNAhybrid miRNA_binding 5797264 5797281 . - . ID="Cluster_15340";energy=-30.09;score=182
## ptg000025l RNAhybrid miRNA_binding 5797264 5797281 . - . ID="Cluster_15340";energy=-30.09;score=182
## ptg000025l RNAhybrid miRNA_binding 5797264 5797281 . - . ID="Cluster_15340";energy=-30.09;score=182
## ptg000012l RNAhybrid miRNA_binding 17288350 17288364 . + . ID="Cluster_15851";energy=-23.52;score=175
## ptg000008l RNAhybrid miRNA_binding 8603023 8603039 . - . ID="Cluster_15854";energy=-24.28;score=181
## ptg000008l RNAhybrid miRNA_binding 8603023 8603039 . - . ID="Cluster_15854";energy=-24.28;score=181
## ptg000008l RNAhybrid miRNA_binding 8603023 8603039 . - . ID="Cluster_15854";energy=-24.28;score=181
## ptg000008l RNAhybrid miRNA_binding 8603023 8603039 . - . ID="Cluster_15854";energy=-24.28;score=181
## ptg000023l RNAhybrid miRNA_binding 7799752 7799770 . - . ID="Cluster_16409";energy=-24.64;score=177
## ntLink_6 RNAhybrid miRNA_binding 4819493 4819515 . - . ID="Cluster_17791";energy=-20.26;score=174
## ntLink_6 RNAhybrid miRNA_binding 4819493 4819515 . - . ID="Cluster_17791";energy=-20.26;score=174
## ntLink_6 RNAhybrid miRNA_binding 4819493 4819515 . - . ID="Cluster_17791";energy=-20.26;score=174
## ntLink_6 RNAhybrid miRNA_binding 4819493 4819515 . - . ID="Cluster_17791";energy=-20.26;score=174
## ptg000021l RNAhybrid miRNA_binding 13589804 13589824 . - . ID="Cluster_1826";energy=-25.71;score=179
## ntLink_8 RNAhybrid miRNA_binding 3046118 3046138 . - . ID="Cluster_1862";energy=-20.09;score=177
## ptg000039l RNAhybrid miRNA_binding 483717 483733 . - . ID="Cluster_19193";energy=-26.35;score=169
## ntLink_8 RNAhybrid miRNA_binding 7813582 7813602 . - . ID="Cluster_2463";energy=-25.95;score=179
## ptg000001l RNAhybrid miRNA_binding 10400679 10400699 . - . ID="Cluster_2463";energy=-25.95;score=178
## ptg000004l RNAhybrid miRNA_binding 11697979 11697993 . - . ID="Cluster_2463";energy=-24.38;score=171
## ptg000007l RNAhybrid miRNA_binding 9978668 9978688 . - . ID="Cluster_2463";energy=-25.95;score=178
## ptg000018l RNAhybrid miRNA_binding 13812471 13812487 . - . ID="Cluster_2463";energy=-24.03;score=169
## ptg000026l RNAhybrid miRNA_binding 7994104 7994124 . - . ID="Cluster_2463";energy=-25.95;score=179
## ntLink_8 RNAhybrid miRNA_binding 20869785 20869806 . + . ID="Cluster_3366";energy=-22.64;score=169
## ntLink_8 RNAhybrid miRNA_binding 20869785 20869806 . + . ID="Cluster_3366";energy=-22.64;score=169
## ntLink_8 RNAhybrid miRNA_binding 30064515 30064532 . + . ID="Cluster_3366";energy=-25.67;score=170
## ntLink_8 RNAhybrid miRNA_binding 30064515 30064532 . + . ID="Cluster_3366";energy=-25.67;score=170
## ptg000020l RNAhybrid miRNA_binding 5862528 5862544 . + . ID="Cluster_3366";energy=-23.94;score=169
## ptg000020l RNAhybrid miRNA_binding 5862528 5862544 . + . ID="Cluster_3366";energy=-23.94;score=169
## ptg000024l RNAhybrid miRNA_binding 9175741 9175760 . + . ID="Cluster_3366";energy=-21.37;score=174
## ptg000024l RNAhybrid miRNA_binding 9175741 9175760 . + . ID="Cluster_3366";energy=-21.37;score=174
## ptg000024l RNAhybrid miRNA_binding 9175741 9175760 . + . ID="Cluster_3366";energy=-21.37;score=174
## ptg000024l RNAhybrid miRNA_binding 9175741 9175760 . + . ID="Cluster_3366";energy=-21.37;score=174
## ptg000036l RNAhybrid miRNA_binding 4523015 4523036 . + . ID="Cluster_3366";energy=-24.55;score=176
## ntLink_8 RNAhybrid miRNA_binding 20869785 20869806 . + . ID="Cluster_3367";energy=-22.64;score=169
## ntLink_8 RNAhybrid miRNA_binding 20869785 20869806 . + . ID="Cluster_3367";energy=-22.64;score=169
## ntLink_8 RNAhybrid miRNA_binding 30064515 30064532 . + . ID="Cluster_3367";energy=-23.68;score=170
## ntLink_8 RNAhybrid miRNA_binding 30064515 30064532 . + . ID="Cluster_3367";energy=-23.68;score=170
## ptg000020l RNAhybrid miRNA_binding 5862528 5862544 . + . ID="Cluster_3367";energy=-25.17;score=169
## ptg000020l RNAhybrid miRNA_binding 5862528 5862544 . + . ID="Cluster_3367";energy=-25.17;score=169
## ptg000024l RNAhybrid miRNA_binding 9175741 9175760 . + . ID="Cluster_3367";energy=-21.37;score=174
## ptg000024l RNAhybrid miRNA_binding 9175741 9175760 . + . ID="Cluster_3367";energy=-21.37;score=174
## ptg000024l RNAhybrid miRNA_binding 9175741 9175760 . + . ID="Cluster_3367";energy=-21.37;score=174
## ptg000024l RNAhybrid miRNA_binding 9175741 9175760 . + . ID="Cluster_3367";energy=-21.37;score=174
## ptg000036l RNAhybrid miRNA_binding 4523015 4523036 . + . ID="Cluster_3367";energy=-22.6;score=176
## ntLink_8 RNAhybrid miRNA_binding 16931011 16931030 . - . ID="Cluster_4220";energy=-30.98;score=188
## ntLink_8 RNAhybrid miRNA_binding 16953818 16953837 . - . ID="Cluster_4220";energy=-30.98;score=188
## ntLink_8 RNAhybrid miRNA_binding 16978257 16978276 . - . ID="Cluster_4220";energy=-30.98;score=188
## ptg000018l RNAhybrid miRNA_binding 1167302 1167318 . - . ID="Cluster_4220";energy=-29.24;score=181
## ptg000035l RNAhybrid miRNA_binding 9011316 9011333 . - . ID="Cluster_4220";energy=-30.63;score=182
## ntLink_6 RNAhybrid miRNA_binding 5772709 5772728 . + . ID="Cluster_4254";energy=-22.88;score=176
## ptg000030l RNAhybrid miRNA_binding 2128306 2128325 . + . ID="Cluster_4254";energy=-24.43;score=178
## ptg000030l RNAhybrid miRNA_binding 2128306 2128325 . + . ID="Cluster_4254";energy=-24.43;score=178
## ptg000030l RNAhybrid miRNA_binding 2128306 2128325 . + . ID="Cluster_4254";energy=-24.43;score=178
## ptg000030l RNAhybrid miRNA_binding 2128306 2128325 . + . ID="Cluster_4254";energy=-24.43;score=178
## ntLink_6 RNAhybrid miRNA_binding 6374246 6374262 . - . ID="Cluster_5012";energy=-26.78;score=185
## ptg000021l RNAhybrid miRNA_binding 16212974 16212995 . - . ID="Cluster_5981";energy=-22.19;score=146
## ptg000021l RNAhybrid miRNA_binding 13589810 13589832 . - . ID=Cluster_1826.mature::ntLink_6:4847465-4847486(-);MFE=-28.7;Pval=0.022695
## ntLink_8 RNAhybrid miRNA_binding 7813588 7813610 . - . ID=Cluster_2463.mature::ptg000001l:5548893-5548914(-);MFE=-27.8;Pval=0.039252
## ptg000001l RNAhybrid miRNA_binding 10400686 10400708 . - . ID=Cluster_2463.mature::ptg000001l:5548893-5548914(-);MFE=-27.8;Pval=0.039252
## ptg000004l RNAhybrid miRNA_binding 11697985 11698007 . - . ID=Cluster_2463.mature::ptg000001l:5548893-5548914(-);MFE=-28.3;Pval=0.030148
## ptg000007l RNAhybrid miRNA_binding 9978675 9978697 . - . ID=Cluster_2463.mature::ptg000001l:5548893-5548914(-);MFE=-27.8;Pval=0.039252
## ptg000018l RNAhybrid miRNA_binding 13812477 13812499 . - . ID=Cluster_2463.mature::ptg000001l:5548893-5548914(-);MFE=-27.8;Pval=0.039252
## ptg000026l RNAhybrid miRNA_binding 7994110 7994132 . - . ID=Cluster_2463.mature::ptg000001l:5548893-5548914(-);MFE=-27.8;Pval=0.039252
## ptg000036l RNAhybrid miRNA_binding 4522999 4523022 . + . ID=Cluster_2859.mature::ptg000001l:20063094-20063116(+);MFE=-26.4;Pval=0.003604
## ptg000036l RNAhybrid miRNA_binding 4522999 4523022 . + . ID=Cluster_2859.mature::ptg000001l:20063094-20063116(+);MFE=-26.4;Pval=0.003604
## ntLink_8 RNAhybrid miRNA_binding 20869798 20869822 . + . ID=Cluster_3366.mature::ptg000002l:14046285-14046308(+);MFE=-21.5;Pval=0.024451
## ntLink_8 RNAhybrid miRNA_binding 20869798 20869822 . + . ID=Cluster_3366.mature::ptg000002l:14046285-14046308(+);MFE=-21.5;Pval=0.024451
## ntLink_8 RNAhybrid miRNA_binding 30064524 30064548 . + . ID=Cluster_3366.mature::ptg000002l:14046285-14046308(+);MFE=-26.9;Pval=0.007283
## ntLink_8 RNAhybrid miRNA_binding 30064524 30064548 . + . ID=Cluster_3366.mature::ptg000002l:14046285-14046308(+);MFE=-26.9;Pval=0.007283
## ptg000020l RNAhybrid miRNA_binding 5862537 5862561 . + . ID=Cluster_3366.mature::ptg000002l:14046285-14046308(+);MFE=-28.8;Pval=0.032792
## ptg000020l RNAhybrid miRNA_binding 5862537 5862561 . + . ID=Cluster_3366.mature::ptg000002l:14046285-14046308(+);MFE=-28.8;Pval=0.032792
## ptg000024l RNAhybrid miRNA_binding 9175751 9175775 . + . ID=Cluster_3366.mature::ptg000002l:14046285-14046308(+);MFE=-26.2;Pval=0.043413
## ptg000024l RNAhybrid miRNA_binding 9175751 9175775 . + . ID=Cluster_3366.mature::ptg000002l:14046285-14046308(+);MFE=-26.2;Pval=0.043413
## ptg000024l RNAhybrid miRNA_binding 9175751 9175775 . + . ID=Cluster_3366.mature::ptg000002l:14046285-14046308(+);MFE=-26.2;Pval=0.043413
## ptg000024l RNAhybrid miRNA_binding 9175751 9175775 . + . ID=Cluster_3366.mature::ptg000002l:14046285-14046308(+);MFE=-26.2;Pval=0.043413
## ptg000024l RNAhybrid miRNA_binding 9175751 9175775 . + . ID=Cluster_3366.mature::ptg000002l:14046285-14046308(+);MFE=-26.2;Pval=0.043413
## ptg000024l RNAhybrid miRNA_binding 9175751 9175775 . + . ID=Cluster_3366.mature::ptg000002l:14046285-14046308(+);MFE=-26.2;Pval=0.043413
## ptg000024l RNAhybrid miRNA_binding 9175751 9175775 . + . ID=Cluster_3366.mature::ptg000002l:14046285-14046308(+);MFE=-26.2;Pval=0.043413
## ptg000024l RNAhybrid miRNA_binding 9175751 9175775 . + . ID=Cluster_3366.mature::ptg000002l:14046285-14046308(+);MFE=-26.2;Pval=0.043413
## ntLink_8 RNAhybrid miRNA_binding 20869798 20869822 . + . ID=Cluster_3367.mature::ptg000002l:14046591-14046614(+);MFE=-21.5;Pval=0.029415
## ntLink_8 RNAhybrid miRNA_binding 20869798 20869822 . + . ID=Cluster_3367.mature::ptg000002l:14046591-14046614(+);MFE=-21.5;Pval=0.029415
## ntLink_8 RNAhybrid miRNA_binding 30064524 30064548 . + . ID=Cluster_3367.mature::ptg000002l:14046591-14046614(+);MFE=-26.9;Pval=0.008933
## ntLink_8 RNAhybrid miRNA_binding 30064524 30064548 . + . ID=Cluster_3367.mature::ptg000002l:14046591-14046614(+);MFE=-26.9;Pval=0.008933
## ptg000020l RNAhybrid miRNA_binding 5862537 5862561 . + . ID=Cluster_3367.mature::ptg000002l:14046591-14046614(+);MFE=-28.8;Pval=0.03925
## ptg000020l RNAhybrid miRNA_binding 5862537 5862561 . + . ID=Cluster_3367.mature::ptg000002l:14046591-14046614(+);MFE=-28.8;Pval=0.03925
## ntLink_8 RNAhybrid miRNA_binding 16931011 16931033 . - . ID=Cluster_4220.mature::ptg000007l:915927-915948(-);MFE=-34.1;Pval=0.0027
## ntLink_8 RNAhybrid miRNA_binding 16953818 16953840 . - . ID=Cluster_4220.mature::ptg000007l:915927-915948(-);MFE=-34.1;Pval=0.0027
## ntLink_8 RNAhybrid miRNA_binding 16978257 16978279 . - . ID=Cluster_4220.mature::ptg000007l:915927-915948(-);MFE=-34.1;Pval=0.0027
## ptg000018l RNAhybrid miRNA_binding 1167306 1167328 . - . ID=Cluster_4220.mature::ptg000007l:915927-915948(-);MFE=-30.4;Pval=0.017938
## ptg000035l RNAhybrid miRNA_binding 9011319 9011341 . - . ID=Cluster_4220.mature::ptg000007l:915927-915948(-);MFE=-30.2;Pval=0.01986
## ntLink_6 RNAhybrid miRNA_binding 5772715 5772737 . + . ID=Cluster_4254.mature::ptg000007l:3377335-3377356(+);MFE=-26.2;Pval=0.025451
## ptg000030l RNAhybrid miRNA_binding 2128313 2128335 . + . ID=Cluster_4254.mature::ptg000007l:3377335-3377356(+);MFE=-26;Pval=0.034916
## ptg000030l RNAhybrid miRNA_binding 2128313 2128335 . + . ID=Cluster_4254.mature::ptg000007l:3377335-3377356(+);MFE=-26;Pval=0.034916
## ptg000030l RNAhybrid miRNA_binding 2128313 2128335 . + . ID=Cluster_4254.mature::ptg000007l:3377335-3377356(+);MFE=-26;Pval=0.034916
## ptg000030l RNAhybrid miRNA_binding 2128313 2128335 . + . ID=Cluster_4254.mature::ptg000007l:3377335-3377356(+);MFE=-26;Pval=0.034916
## ntLink_6 RNAhybrid miRNA_binding 6374249 6374270 . - . ID=Cluster_5012.mature::ptg000008l:10754789-10754809(-);MFE=-31;Pval=0.007748
## ptg000019l RNAhybrid miRNA_binding 3905999 3906021 . + . ID=Cluster_10051.mature::ptg000016l:7795530-7795551(+);MFE=-25.5;Pval=0.013755
## ptg000039l RNAhybrid miRNA_binding 1038032 1038054 . + . ID=Cluster_10051.mature::ptg000016l:7795530-7795551(+);MFE=-29;Pval=0.020136
## ntLink_8 RNAhybrid miRNA_binding 17362806 17362828 . - . ID=Cluster_10057.mature::ptg000016l:8599884-8599905(-);MFE=-28.6;Pval=0.036082
## ptg000008l RNAhybrid miRNA_binding 6343729 6343751 . - . ID=Cluster_10057.mature::ptg000016l:8599884-8599905(-);MFE=-28.2;Pval=0.044287
## ptg000015l RNAhybrid miRNA_binding 2404079 2404101 . - . ID=Cluster_10057.mature::ptg000016l:8599884-8599905(-);MFE=-28.2;Pval=0.044287
## ptg000026l RNAhybrid miRNA_binding 556252 556274 . - . ID=Cluster_10057.mature::ptg000016l:8599884-8599905(-);MFE=-28.6;Pval=0.036082
## ptg000026l RNAhybrid miRNA_binding 896128 896150 . - . ID=Cluster_10057.mature::ptg000016l:8599884-8599905(-);MFE=-28.6;Pval=0.036082
## ptg000047l RNAhybrid miRNA_binding 2819158 2819180 . - . ID=Cluster_10093.mature::ptg000016l:11751407-11751428(-);MFE=-30.4;Pval=0.012598
## ptg000047l RNAhybrid miRNA_binding 2819158 2819180 . - . ID=Cluster_10093.mature::ptg000016l:11751407-11751428(-);MFE=-30.4;Pval=0.012598
## ptg000047l RNAhybrid miRNA_binding 2819158 2819180 . - . ID=Cluster_10093.mature::ptg000016l:11751407-11751428(-);MFE=-30.4;Pval=0.012598
## ptg000047l RNAhybrid miRNA_binding 2819158 2819180 . - . ID=Cluster_10093.mature::ptg000016l:11751407-11751428(-);MFE=-30.4;Pval=0.012598
## ptg000021l RNAhybrid miRNA_binding 13553487 13553508 . + . ID=Cluster_14768.mature::ptg000023l:37965298-37965318(+);MFE=-41.5;Pval=0.000033
## ptg000021l RNAhybrid miRNA_binding 16212956 16212977 . + . ID=Cluster_14768.mature::ptg000023l:37965298-37965318(+);MFE=-27.9;Pval=0.009385
## ntLink_6 RNAhybrid miRNA_binding 15902888 15902910 . + . ID=Cluster_15316.mature::ptg000024l:4086254-4086275(+);MFE=-28.7;Pval=0.034534
## ptg000034l RNAhybrid miRNA_binding 183630 183652 . + . ID=Cluster_15316.mature::ptg000024l:4086254-4086275(+);MFE=-30.8;Pval=0.011661
## ptg000064l RNAhybrid miRNA_binding 99593 99615 . + . ID=Cluster_15316.mature::ptg000024l:4086254-4086275(+);MFE=-30.8;Pval=0.011661
## ntLink_8 RNAhybrid miRNA_binding 17362805 17362827 . - . ID=Cluster_15340.mature::ptg000024l:5256476-5256497(-);MFE=-29.5;Pval=0.031681
## ntLink_8 RNAhybrid miRNA_binding 31354517 31354539 . - . ID=Cluster_15340.mature::ptg000024l:5256476-5256497(-);MFE=-28.9;Pval=0.04276
## ptg000002l RNAhybrid miRNA_binding 3411170 3411192 . - . ID=Cluster_15340.mature::ptg000024l:5256476-5256497(-);MFE=-29;Pval=0.04068
## ptg000009l RNAhybrid miRNA_binding 10224592 10224614 . - . ID=Cluster_15340.mature::ptg000024l:5256476-5256497(-);MFE=-28.9;Pval=0.04276
## ptg000011l RNAhybrid miRNA_binding 11819551 11819573 . - . ID=Cluster_15340.mature::ptg000024l:5256476-5256497(-);MFE=-30.6;Pval=0.018216
## ptg000015l RNAhybrid miRNA_binding 2404078 2404100 . - . ID=Cluster_15340.mature::ptg000024l:5256476-5256497(-);MFE=-30.2;Pval=0.022286
## ptg000020l RNAhybrid miRNA_binding 16091592 16091614 . - . ID=Cluster_15340.mature::ptg000024l:5256476-5256497(-);MFE=-30.3;Pval=0.021191
## ptg000020l RNAhybrid miRNA_binding 16493605 16493627 . - . ID=Cluster_15340.mature::ptg000024l:5256476-5256497(-);MFE=-32.2;Pval=0.008105
## ptg000023l RNAhybrid miRNA_binding 24634245 24634267 . - . ID=Cluster_15340.mature::ptg000024l:5256476-5256497(-);MFE=-31.9;Pval=0.009436
## ptg000025l RNAhybrid miRNA_binding 1210284 1210306 . - . ID=Cluster_15340.mature::ptg000024l:5256476-5256497(-);MFE=-31.3;Pval=0.012788
## ptg000025l RNAhybrid miRNA_binding 5797267 5797289 . - . ID=Cluster_15340.mature::ptg000024l:5256476-5256497(-);MFE=-31.8;Pval=0.008009
## ptg000025l RNAhybrid miRNA_binding 5797267 5797289 . - . ID=Cluster_15340.mature::ptg000024l:5256476-5256497(-);MFE=-31.8;Pval=0.008009
## ptg000025l RNAhybrid miRNA_binding 5797267 5797289 . - . ID=Cluster_15340.mature::ptg000024l:5256476-5256497(-);MFE=-31.8;Pval=0.008009
## ptg000025l RNAhybrid miRNA_binding 5797267 5797289 . - . ID=Cluster_15340.mature::ptg000024l:5256476-5256497(-);MFE=-31.8;Pval=0.008009
## ptg000026l RNAhybrid miRNA_binding 556251 556273 . - . ID=Cluster_15340.mature::ptg000024l:5256476-5256497(-);MFE=-31.2;Pval=0.013451
## ptg000026l RNAhybrid miRNA_binding 896127 896149 . - . ID=Cluster_15340.mature::ptg000024l:5256476-5256497(-);MFE=-31.2;Pval=0.013451
## ptg000036l RNAhybrid miRNA_binding 859245 859267 . - . ID=Cluster_15340.mature::ptg000024l:5256476-5256497(-);MFE=-31;Pval=0.014883
## ptg000012l RNAhybrid miRNA_binding 17288356 17288378 . + . ID=Cluster_15851.mature::ptg000025l:10501052-10501073(+);MFE=-29;Pval=0.022003
## ptg000008l RNAhybrid miRNA_binding 8603028 8603051 . - . ID=Cluster_15854.mature::ptg000025l:10668923-10668945(-);MFE=-27.3;Pval=0.021392
## ptg000008l RNAhybrid miRNA_binding 8603028 8603051 . - . ID=Cluster_15854.mature::ptg000025l:10668923-10668945(-);MFE=-27.3;Pval=0.021392
## ptg000008l RNAhybrid miRNA_binding 8603028 8603051 . - . ID=Cluster_15854.mature::ptg000025l:10668923-10668945(-);MFE=-27.3;Pval=0.021392
## ptg000008l RNAhybrid miRNA_binding 8603028 8603051 . - . ID=Cluster_15854.mature::ptg000025l:10668923-10668945(-);MFE=-27.3;Pval=0.021392
## ptg000023l RNAhybrid miRNA_binding 7799756 7799778 . - . ID=Cluster_16409.mature::ptg000026l:8745562-8745583(-);MFE=-27.7;Pval=0.04698
## ntLink_8 RNAhybrid miRNA_binding 3046116 3046138 . - . ID=Cluster_17776.mature::ptg000031l:5461327-5461348(-);MFE=-29.4;Pval=0.001937
## ntLink_6 RNAhybrid miRNA_binding 4819483 4819506 . - . ID=Cluster_17791.mature::ptg000031l:6751957-6751979(-);MFE=-21.9;Pval=0.022713
## ntLink_6 RNAhybrid miRNA_binding 4819483 4819506 . - . ID=Cluster_17791.mature::ptg000031l:6751957-6751979(-);MFE=-21.9;Pval=0.022713
## ntLink_6 RNAhybrid miRNA_binding 4819483 4819506 . - . ID=Cluster_17791.mature::ptg000031l:6751957-6751979(-);MFE=-21.9;Pval=0.022713
## ntLink_6 RNAhybrid miRNA_binding 4819483 4819506 . - . ID=Cluster_17791.mature::ptg000031l:6751957-6751979(-);MFE=-21.9;Pval=0.022713
## ptg000039l RNAhybrid miRNA_binding 483724 483746 . - . ID=Cluster_19193.mature::ptg000039l:35786-35807(-);MFE=-28.3;Pval=0.04365miRanda_RNAhybrid_miRNA_mRNA <- left_join(miRanda_miRNA_mRNA, RNAhybrid_miRNA_mRNA, by = c("miRNA_cluster" = "target_name"))