Kathleen’s Lab Notebook - Deep Dive Expression: Results Wrap-up

Trying to wrap up the results section for this manuscript!

library(dplyr)

Warning: package 'dplyr' was built under R version 4.2.3


Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

To-Do List:

Confirm mRNA results #s
mRNA GO slim top 20 in each species — think I assigned this to Sam
lncRNA results #s – should go to Zach
miRNA results – fill in counts
lncRNA-mRNA interactions. Need to do lncRNA-mRNA PCC on all three species, or see whether Zach has done it

miRNA-mRNA interactions.

For all three species, summarize binding and PCC

Apul_PCC_miRNA_mRNA <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/D-Apul/output/09-Apul-mRNA-miRNA-interactions/Apul-PCC_miRNA_mRNA.csv")
print("# Apul miRNA-mRNA PCC values signficant at p<0.05:")

[1] "# Apul miRNA-mRNA PCC values signficant at p<0.05:"

Apul_PCC_miRNA_mRNA %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 66154

cat("\n")

miranda_strict_all_1kb_parsed_apul_updated <- read.table("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/D-Apul/output/09-Apul-mRNA-miRNA-interactions/miranda_strict_all_1kb_parsed_apul_updated.txt")
print("# Apul miRNA-3UTR miRanda interactions:")

[1] "# Apul miRNA-3UTR miRanda interactions:"

nrow(miranda_strict_all_1kb_parsed_apul_updated)

[1] 6109

print("Average miRanda total bp shared:")

[1] "Average miRanda total bp shared:"

mean(miranda_strict_all_1kb_parsed_apul_updated$V9)

[1] 18.93354

print("SD of miRanda total bp shared")

[1] "SD of miRanda total bp shared"

sd(miranda_strict_all_1kb_parsed_apul_updated$V9)

[1] 3.311166

cat("\n")

Apul_miRanda_5UTR_1kb_strict_parsed <- read.table("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/D-Apul/output/09.01-Apul-mRNA-miRNA-interactions-CDS_5UTR/Apul-miRanda-5UTR_1kb-strict-parsed.txt")
print("# Apul miRNA-5UTR miRanda interactions:")

[1] "# Apul miRNA-5UTR miRanda interactions:"

nrow(Apul_miRanda_5UTR_1kb_strict_parsed)

[1] 4959

print("Average miRanda total bp shared:")

[1] "Average miRanda total bp shared:"

mean(Apul_miRanda_5UTR_1kb_strict_parsed$V9)

[1] 18.83565

print("SD of miRanda total bp shared")

[1] "SD of miRanda total bp shared"

sd(Apul_miRanda_5UTR_1kb_strict_parsed$V9)

[1] 3.580151

cat("\n")

Apul_miRanda_mRNA_full_strict_parsed <- read.table("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/D-Apul/output/09.01-Apul-mRNA-miRNA-interactions-CDS_5UTR/Apul-miRanda-mRNA_full-strict-parsed.txt")
print("# Apul miRNA-CDS miRanda interactions:")

[1] "# Apul miRNA-CDS miRanda interactions:"

nrow(Apul_miRanda_mRNA_full_strict_parsed)

[1] 38152

print("Average miRanda total bp shared:")

[1] "Average miRanda total bp shared:"

mean(Apul_miRanda_mRNA_full_strict_parsed$V9)

[1] 18.88687

print("SD of miRanda total bp shared")

[1] "SD of miRanda total bp shared"

sd(Apul_miRanda_mRNA_full_strict_parsed$V9)

[1] 3.519626

cat("\n")

Apul_miranda_PCC_miRNA_3UTR <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/D-Apul/output/09-Apul-mRNA-miRNA-interactions/miranda_PCC_miRNA_mRNA.csv")
Apul_miranda_PCC_miRNA_5UTR <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/D-Apul/output/09.01-Apul-mRNA-miRNA-interactions-CDS_5UTR/miRanda_PCC_miRNA_5UTR.csv")
Apul_miranda_PCC_miRNA_CDS <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/D-Apul/output/09.01-Apul-mRNA-miRNA-interactions-CDS_5UTR/miRanda_PCC_miRNA_CDS.csv")

print("# Apul miRNA-3UTR miRanda interactions WITH significant PCC (pval < 0.05)")

[1] "# Apul miRNA-3UTR miRanda interactions WITH significant PCC (pval < 0.05)"

Apul_miranda_PCC_miRNA_3UTR %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 266

print("# Apul miRNA-5UTR miRanda interactions WITH significant PCC (pval < 0.05)")

[1] "# Apul miRNA-5UTR miRanda interactions WITH significant PCC (pval < 0.05)"

Apul_miranda_PCC_miRNA_5UTR %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 217

print("# Apul miRNA-CDS miRanda interactions WITH significant PCC (pval < 0.05)")

[1] "# Apul miRNA-CDS miRanda interactions WITH significant PCC (pval < 0.05)"

Apul_miranda_PCC_miRNA_CDS %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 1739

Peve_PCC_miRNA_mRNA <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/E-Peve/output/10-Peve-mRNA-miRNA-interactions/Peve-PCC_miRNA_mRNA.csv")
print("# Peve miRNA-mRNA PCC values signficant at p<0.05:")

[1] "# Peve miRNA-mRNA PCC values signficant at p<0.05:"

Peve_PCC_miRNA_mRNA %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 69580

cat("\n")

miranda_strict_all_1kb_parsed_Peve_updated <- read.table("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/E-Peve/output/10-Peve-mRNA-miRNA-interactions/miranda_strict_all_1kb_parsed_peve_updated.txt")
print("# Peve miRNA-3UTR miRanda interactions:")

[1] "# Peve miRNA-3UTR miRanda interactions:"

nrow(miranda_strict_all_1kb_parsed_Peve_updated)

[1] 5067

print("Average miRanda total bp shared:")

[1] "Average miRanda total bp shared:"

mean(miranda_strict_all_1kb_parsed_Peve_updated$V9)

[1] 18.22558

print("SD of miRanda total bp shared")

[1] "SD of miRanda total bp shared"

sd(miranda_strict_all_1kb_parsed_Peve_updated$V9)

[1] 3.384178

cat("\n")

Peve_miRanda_5UTR_1kb_strict_parsed <- read.table("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/E-Peve/output/10.01-Peve-mRNA-miRNA-interactions-CDS_5UTR/Peve-miRanda-5UTR_1kb-strict-parsed.txt")
print("# Peve miRNA-5UTR miRanda interactions:")

[1] "# Peve miRNA-5UTR miRanda interactions:"

nrow(Peve_miRanda_5UTR_1kb_strict_parsed)

[1] 5054

print("Average miRanda total bp shared:")

[1] "Average miRanda total bp shared:"

mean(Peve_miRanda_5UTR_1kb_strict_parsed$V9)

[1] 18.10388

print("SD of miRanda total bp shared")

[1] "SD of miRanda total bp shared"

sd(Peve_miRanda_5UTR_1kb_strict_parsed$V9)

[1] 3.503256

cat("\n")

Peve_miRanda_mRNA_full_strict_parsed <- read.table("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/E-Peve/output/10.01-Peve-mRNA-miRNA-interactions-CDS_5UTR/Peve-miRanda-mRNA_full-strict-parsed.txt")
print("# Peve miRNA-CDS miRanda interactions:")

[1] "# Peve miRNA-CDS miRanda interactions:"

nrow(Peve_miRanda_mRNA_full_strict_parsed)

[1] 13934

print("Average miRanda total bp shared:")

[1] "Average miRanda total bp shared:"

mean(Peve_miRanda_mRNA_full_strict_parsed$V9)

[1] 18.12846

print("SD of miRanda total bp shared")

[1] "SD of miRanda total bp shared"

sd(Peve_miRanda_mRNA_full_strict_parsed$V9)

[1] 3.660678

cat("\n")

Peve_miranda_PCC_miRNA_3UTR <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/E-Peve/output/10-Peve-mRNA-miRNA-interactions/Peve-miranda_PCC_miRNA_mRNA.csv")
Peve_miranda_PCC_miRNA_5UTR <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/E-Peve/output/10.01-Peve-mRNA-miRNA-interactions-CDS_5UTR/miRanda_PCC_miRNA_5UTR.csv")
Peve_miranda_PCC_miRNA_CDS <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/E-Peve/output/10.01-Peve-mRNA-miRNA-interactions-CDS_5UTR/miRanda_PCC_miRNA_CDS.csv")

print("# Peve miRNA-3UTR miRanda interactions WITH significant PCC (pval < 0.05)")

[1] "# Peve miRNA-3UTR miRanda interactions WITH significant PCC (pval < 0.05)"

Peve_miranda_PCC_miRNA_3UTR %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 208

print("# Peve miRNA-5UTR miRanda interactions WITH significant PCC (pval < 0.05)")

[1] "# Peve miRNA-5UTR miRanda interactions WITH significant PCC (pval < 0.05)"

Peve_miranda_PCC_miRNA_5UTR %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 224

print("# Peve miRNA-CDS miRanda interactions WITH significant PCC (pval < 0.05)")

[1] "# Peve miRNA-CDS miRanda interactions WITH significant PCC (pval < 0.05)"

Peve_miranda_PCC_miRNA_CDS %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 835

Ptuh_PCC_miRNA_mRNA <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/F-Ptuh/output/11-Ptuh-mRNA-miRNA-interactions/three_prime_interaction/Ptuh-PCC_miRNA_mRNA.csv")
print("# Ptuh miRNA-mRNA PCC values signficant at p<0.05:")

[1] "# Ptuh miRNA-mRNA PCC values signficant at p<0.05:"

Ptuh_PCC_miRNA_mRNA %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 61866

cat("\n")

miranda_strict_all_1kb_parsed_Ptuh_updated <- read.table("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/F-Ptuh/output/11-Ptuh-mRNA-miRNA-interactions/three_prime_interaction/miranda_strict_all_1kb_parsed_ptuh_updated.txt")
print("# Ptuh miRNA-3UTR miRanda interactions:")

[1] "# Ptuh miRNA-3UTR miRanda interactions:"

nrow(miranda_strict_all_1kb_parsed_Ptuh_updated)

[1] 4105

print("Average miRanda total bp shared:")

[1] "Average miRanda total bp shared:"

mean(miranda_strict_all_1kb_parsed_Ptuh_updated$V9)

[1] 18.39026

print("SD of miRanda total bp shared")

[1] "SD of miRanda total bp shared"

sd(miranda_strict_all_1kb_parsed_Ptuh_updated$V9)

[1] 3.116516

cat("\n")

Ptuh_miRanda_5UTR_1kb_strict_parsed <- read.table("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/F-Ptuh/output/11.01-Ptuh-mRNA-miRNA-interactions-CDS_5UTR/Ptuh-miRanda-5UTR_1kb-strict-parsed.txt")
print("# Ptuh miRNA-5UTR miRanda interactions:")

[1] "# Ptuh miRNA-5UTR miRanda interactions:"

nrow(Ptuh_miRanda_5UTR_1kb_strict_parsed)

[1] 3881

print("Average miRanda total bp shared:")

[1] "Average miRanda total bp shared:"

mean(Ptuh_miRanda_5UTR_1kb_strict_parsed$V9)

[1] 18.29915

print("SD of miRanda total bp shared")

[1] "SD of miRanda total bp shared"

sd(Ptuh_miRanda_5UTR_1kb_strict_parsed$V9)

[1] 3.256227

cat("\n")

Ptuh_miRanda_mRNA_full_strict_parsed <- read.table("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/F-Ptuh/output/11.01-Ptuh-mRNA-miRNA-interactions-CDS_5UTR/Ptuh-miRanda-mRNA_full-strict-parsed.txt")
print("# Ptuh miRNA-CDS miRanda interactions:")

[1] "# Ptuh miRNA-CDS miRanda interactions:"

nrow(Ptuh_miRanda_mRNA_full_strict_parsed)

[1] 9537

print("Average miRanda total bp shared:")

[1] "Average miRanda total bp shared:"

mean(Ptuh_miRanda_mRNA_full_strict_parsed$V9)

[1] 18.69319

print("SD of miRanda total bp shared")

[1] "SD of miRanda total bp shared"

sd(Ptuh_miRanda_mRNA_full_strict_parsed$V9)

[1] 3.150355

cat("\n")

Ptuh_miranda_PCC_miRNA_3UTR <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/F-Ptuh/output/11-Ptuh-mRNA-miRNA-interactions/three_prime_interaction/Ptuh-miranda_PCC_miRNA_mRNA.csv")
Ptuh_miranda_PCC_miRNA_5UTR <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/F-Ptuh/output/11.01-Ptuh-mRNA-miRNA-interactions-CDS_5UTR/miRanda_PCC_miRNA_5UTR.csv")
Ptuh_miranda_PCC_miRNA_CDS <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/F-Ptuh/output/11.01-Ptuh-mRNA-miRNA-interactions-CDS_5UTR/miRanda_PCC_miRNA_CDS.csv")

print("# Ptuh miRNA-3UTR miRanda interactions WITH significant PCC (pval < 0.05)")

[1] "# Ptuh miRNA-3UTR miRanda interactions WITH significant PCC (pval < 0.05)"

Ptuh_miranda_PCC_miRNA_3UTR %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 203

print("# Ptuh miRNA-5UTR miRanda interactions WITH significant PCC (pval < 0.05)")

[1] "# Ptuh miRNA-5UTR miRanda interactions WITH significant PCC (pval < 0.05)"

Ptuh_miranda_PCC_miRNA_5UTR %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 200

print("# Ptuh miRNA-CDS miRanda interactions WITH significant PCC (pval < 0.05)")

[1] "# Ptuh miRNA-CDS miRanda interactions WITH significant PCC (pval < 0.05)"

Ptuh_miranda_PCC_miRNA_CDS %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 499

Warning

Need to check with Jill how the above miRanda results were generated. Points of concern are

Were inputs 3UTR sites only, or all three 3UTR, 5UTR, and CDS regions?
What were the significance parameters? Was there a cutoff for minimum total bp shared?

^Looks like Jill only used the miRanda settings -e -20 and -strict, while I used -e -20, -sc 100, and -strict. The -sc is a score cutoff. It may not have affected results, since a brief check suggested the energy cutoff (-e -20) was more stringent and implicitly restricted results to scores above 100. However, I should add a manual filter when using Jill’s miRanda outputs (miRNA-3UTR) to be safe.

We also have topGO enrichment of significant miRNA-mRNA interactions if we want to use them

miRNA-lncRNA interactions.

For all three species, summarize binding and PCC. overlap among species

Apul_PCC_miRNA_lncRNA <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/D-Apul/output/28-Apul-miRNA-lncRNA-interactions/Apul-PCC_miRNA_lncRNA.csv")
print("# Apul miRNA-lncRNA PCC values signficant at p<0.05:")

[1] "# Apul miRNA-lncRNA PCC values signficant at p<0.05:"

Apul_PCC_miRNA_lncRNA %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 53804

Apul_miRanda_lncRNA_strict_parsed <- read.table("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/D-Apul/output/17-Apul-miRNA-lncRNA-BLASTs-RNAhybrid/Apul-miRanda-lncRNA-strict-parsed.txt")
print("# Apul miRNA-lncRNA miRanda interactions:")

[1] "# Apul miRNA-lncRNA miRanda interactions:"

nrow(Apul_miRanda_lncRNA_strict_parsed)

[1] 12390

print("Average miRanda total bp shared:")

[1] "Average miRanda total bp shared:"

mean(Apul_miRanda_lncRNA_strict_parsed$V9)

[1] 17.52881

print("SD of miRanda total bp shared")

[1] "SD of miRanda total bp shared"

sd(Apul_miRanda_lncRNA_strict_parsed$V9)

[1] 4.562401

cat("\n")

Apul_lncRNA_to_precursor_blastn <- read.table("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/D-Apul/output/17-Apul-miRNA-lncRNA-BLASTs-RNAhybrid/blasts/lncRNA_to_precursor_blastn.tab")
colnames(Apul_lncRNA_to_precursor_blastn) <- c("qseqid", "sseqid", "pident", "length", "mismatch", "gapopen", "qstart", "qend", "sstart", "send", "evalue", "bitscore")
print("# Apul lncRNA that contain full pre-miRNA")

[1] "# Apul lncRNA that contain full pre-miRNA"

Apul_lncRNA_to_precursor_blastn %>% filter(length >= 90) %>% filter(mismatch == 0) %>% nrow()

[1] 7

print("Note: the above value includes lncRNA that have highly overlapping genomic coordinates, suggesting instances of isoforms of the same lncRNA")

[1] "Note: the above value includes lncRNA that have highly overlapping genomic coordinates, suggesting instances of isoforms of the same lncRNA"

cat("\n")

Apul_miranda_PCC_miRNA_lncRNA <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/D-Apul/output/28-Apul-miRNA-lncRNA-interactions/miranda_PCC_miRNA_lncRNA.csv")
print("# Apul miRNA-lncRNA miRanda interactions WITH significant PCC (pval < 0.05)")

[1] "# Apul miRNA-lncRNA miRanda interactions WITH significant PCC (pval < 0.05)"

Apul_miranda_PCC_miRNA_lncRNA %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 365

Peve_PCC_miRNA_lncRNA <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/E-Peve/output/15-Peve-miRNA-lncRNA-PCC/PCC_miRNA_lncRNA.csv")
print("# Peve miRNA-lncRNA PCC values signficant at p<0.05:")

[1] "# Peve miRNA-lncRNA PCC values signficant at p<0.05:"

Peve_PCC_miRNA_lncRNA %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 15705

Peve_miRanda_lncRNA_strict_parsed <- read.table("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/E-Peve/output/14-Peve-miRNA-lncRNA-BLASTs-miRanda/Peve-miRanda-lncRNA-strict-parsed.txt")
print("# Peve miRNA-lncRNA miRanda interactions:")

[1] "# Peve miRNA-lncRNA miRanda interactions:"

nrow(Peve_miRanda_lncRNA_strict_parsed)

[1] 4116

print("Average miRanda total bp shared:")

[1] "Average miRanda total bp shared:"

mean(Peve_miRanda_lncRNA_strict_parsed$V9)

[1] 17.91399

print("SD of miRanda total bp shared")

[1] "SD of miRanda total bp shared"

sd(Peve_miRanda_lncRNA_strict_parsed$V9)

[1] 3.491269

cat("\n")

Peve_lncRNA_to_precursor_blastn <- read.table("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/E-Peve/output/14-Peve-miRNA-lncRNA-BLASTs-miRanda/blasts/lncRNA_to_precursor_blastn.tab")
colnames(Peve_lncRNA_to_precursor_blastn) <- c("qseqid", "sseqid", "pident", "length", "mismatch", "gapopen", "qstart", "qend", "sstart", "send", "evalue", "bitscore")
print("# Peve lncRNA that contain full pre-miRNA")

[1] "# Peve lncRNA that contain full pre-miRNA"

Peve_lncRNA_to_precursor_blastn %>% filter(length >= 90) %>% filter(mismatch == 0) %>% nrow()

[1] 2

print("Note: the above value includes lncRNA that have highly overlapping genomic coordinates, suggesting instances of isoforms of the same lncRNA")

[1] "Note: the above value includes lncRNA that have highly overlapping genomic coordinates, suggesting instances of isoforms of the same lncRNA"

cat("\n")

Peve_miranda_PCC_miRNA_lncRNA <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/E-Peve/output/15-Peve-miRNA-lncRNA-PCC/miranda_PCC_miRNA_lncRNA.csv")
print("# Peve miRNA-lncRNA miRanda interactions WITH significant PCC (pval < 0.05)")

[1] "# Peve miRNA-lncRNA miRanda interactions WITH significant PCC (pval < 0.05)"

Peve_miranda_PCC_miRNA_lncRNA %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 118

Ptuh_PCC_miRNA_lncRNA <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/F-Ptuh/output/15-Ptuh-miRNA-lncRNA-PCC/PCC_miRNA_lncRNA.csv")
print("# Ptuh miRNA-lncRNA PCC values signficant at p<0.05:")

[1] "# Ptuh miRNA-lncRNA PCC values signficant at p<0.05:"

Ptuh_PCC_miRNA_lncRNA %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 34959

Ptuh_miRanda_lncRNA_strict_parsed <- read.table("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/F-Ptuh/output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh-miRanda-lncRNA-strict-parsed.txt")
print("# Ptuh miRNA-lncRNA miRanda interactions:")

[1] "# Ptuh miRNA-lncRNA miRanda interactions:"

nrow(Ptuh_miRanda_lncRNA_strict_parsed)

[1] 8341

print("Average miRanda total bp shared:")

[1] "Average miRanda total bp shared:"

mean(Ptuh_miRanda_lncRNA_strict_parsed$V9)

[1] 18.51145

print("SD of miRanda total bp shared")

[1] "SD of miRanda total bp shared"

sd(Ptuh_miRanda_lncRNA_strict_parsed$V9)

[1] 3.119947

cat("\n")

Ptuh_lncRNA_to_precursor_blastn <- read.table("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/F-Ptuh/output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/blasts/lncRNA_to_precursor_blastn.tab")
colnames(Ptuh_lncRNA_to_precursor_blastn) <- c("qseqid", "sseqid", "pident", "length", "mismatch", "gapopen", "qstart", "qend", "sstart", "send", "evalue", "bitscore")
print("# Ptuh lncRNA that contain full pre-miRNA")

[1] "# Ptuh lncRNA that contain full pre-miRNA"

Ptuh_lncRNA_to_precursor_blastn %>% filter(length >= 90) %>% filter(mismatch == 0) %>% nrow()

[1] 8

print("Note: the above value includes lncRNA that have highly overlapping genomic coordinates, suggesting instances of isoforms of the same lncRNA")

[1] "Note: the above value includes lncRNA that have highly overlapping genomic coordinates, suggesting instances of isoforms of the same lncRNA"

cat("\n")

Ptuh_miranda_PCC_miRNA_lncRNA <- read.csv("https://gannet.fish.washington.edu/kdurkin1/ravenbackups/deep-dive-expression/F-Ptuh/output/15-Ptuh-miRNA-lncRNA-PCC/miranda_PCC_miRNA_lncRNA.csv")
print("# Ptuh miRNA-lncRNA miRanda interactions WITH significant PCC (pval < 0.05)")

[1] "# Ptuh miRNA-lncRNA miRanda interactions WITH significant PCC (pval < 0.05)"

Ptuh_miranda_PCC_miRNA_lncRNA %>% filter(p_value < 0.05) %>% unique() %>% nrow()

[1] 352

precursors - PCC

Should validate lncRNA acting as miRNA precursors by checking for coexpression

miRNA-mRNA interactions.

miRNA-lncRNA interactions.

lncRNA-mRNA-miRNA