MicroRNA and Salmo Salar

Introduction

GC and SK sent samples to Arraystar, Rockville MD for miRNA analysis. What follows is an attempt to make sense of the results.

outline of pipeline

• miRNA Expression Profiling
• Novel miRNA detection
• Differentially expressed miRNAs
• miRNA target prediction
• Pathway Analysis

Excel files in results

Tools

Specific cells must be extracted from Excel files so that matching of data can occur between them.

• use Gnumeric's ssconvert to convert to TSV
• delete the explanatory rows at the top, so that the first row is the header (titles of the columns)
• use papath.py python script to match up genes implicated in pathways with the miRNA's target gene list

Listings

We can use this listing to see miRNAs and files of interest

mirRNA Expression Profiling

./miRNA_Expression_Profiling/All_Comparisons_of_Expressed_miRNAs.xls
./miRNA_Expression_Profiling/miRNA_Expression_Analysis.xls

Novel miRNAs

./Novel_miRNAs/novel_miRNAs_predicted_by_miRDeep2.xls

Differentially expressed miRNAs

./Differentially_Expressed_miRNAs/Differentially_Expressed_miRNAs.xls

Initial target prediction

./miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-132-5p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-132-5p/Target Sites.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-23b-5p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-23b-5p/Target Sites.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-30e-5p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-30e-5p/Target Sites.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-8157-3p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-8157-3p/Target Sites.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-let-7c-3p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-let-7c-3p/Target Sites.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-let-7d-3p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-let-7d-3p/Target Sites.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-146a-3p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-146a-3p/Target Sites.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-222b-5p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-222b-5p/Target Sites.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-731-3p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-731-3p/Target Sites.xls

Initial pathway Analysis

./Pathway_Analysis_Results__miRNA_Targets_/Smolt_vs_Parr_down.mature_mirna/sas_pathwayResult.xls
./Pathway_Analysis_Results__miRNA_Targets_/Smolt_vs_Parr_up.mature_mirna/sas_pathwayResult.xls

Supplemental target prediction

./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-23b-5p/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-23b-5p/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-8157-3p/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-8157-3p/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-novel-AGKD03020525.1_11615/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-novel-AGKD03020525.1_11615/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-novel-AGKD03067625.1_26128/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-novel-AGKD03067625.1_26128/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-novel-AGKD03074379.1_27027/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-novel-AGKD03074379.1_27027/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-novel-AGKD03101962.1_28818/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-novel-AGKD03101962.1_28818/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-222b-5p/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-222b-5p/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-731-3p/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-731-3p/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-novel-AGKD03022511.1_12826/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-novel-AGKD03022511.1_12826/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-novel-AGKD03052739.1_23807/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-novel-AGKD03052739.1_23807/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-novel-AGKD03052741.1_23813/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-novel-AGKD03052741.1_23813/Target Sites.xls

Supplemental Pathway Analysis

./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/Pathway Analysis/down.mature_mirna/sas_pathwayResult.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/Pathway Analysis/up.mature_mirna/sas_pathwayResult.xls

In summary

miRNAs of interest are as follows:

Initial target prediction

Down-regulated:
ssa-miR-132-5p
ssa-miR-23b-5p
ssa-miR-30e-5p
ssa-miR-8157-3p
Up-regulated:
ssa-let-7c-3p
ssa-let-7d-3p
ssa-miR-146a-3p
ssa-miR-222b-5p
ssa-miR-731-3p

Supplemental target prediction

Down-regulated:
ssa-miR-23b-5p
ssa-miR-8157-3p
ssa-miR-novel-AGKD03020525.1_11615
ssa-miR-novel-AGKD03067625.1_26128
ssa-miR-novel-AGKD03074379.1_27027
ssa-miR-novel-AGKD03101962.1_28818
Up-regulated:
ssa-miR-222b-5p
ssa-miR-731-3p
ssa-miR-novel-AGKD03022511.1_12826
ssa-miR-novel-AGKD03052739.1_23807
ssa-miR-novel-AGKD03052741.1_23813

miRNA targeted genes implicated in pathways

222b-5p (up-regulated)

Initial files: 1252 genes in target file, of which 30 are implicated in pathways:

LOC106589938:  XM_014180388 sasa00770 | 
LOC106589938:  XM_014180389 sasa00770 | 
LOC106588562:  XM_014177695 sasa04512 | 
LOC106563775:  XM_014129626 sasa04514 | 
LOC106581797:  XM_014164110 sasa00140 | 
LOC106567193:  XM_014136206 sasa03015 | 
LOC106607326:  XM_014204186 sasa04672 | 
LOC106570581:  XM_014143031 sasa04933 |  XM_014143031 sasa04672 | 
LOC106561972:  XM_014126469 sasa04933 | 
LOC106561972:  XM_014126470 sasa04933 | 
LOC106578082:  XM_014156667 sasa03015 | 
LOC106572405:  XM_014146541 sasa04514 | 
LOC100380852:  XM_014204668 sasa00770 | 
LOC106605368:  XM_014200901 sasa04514 | 
LOC106605368:  XM_014200902 sasa04514 |  
LOC106560399:  XM_014123279 sasa04933 | 
LOC106560399:  XM_014123281 sasa04933 | 
LOC106578834:  XM_014158031 sasa00770 | 
LOC106578834:  XM_014158032 sasa00770 | 
LOC106578834:  XM_014158033 sasa00770 | 
LOC106578834:  XM_014158034 sasa00770 | 
LOC106578834:  XM_014158036 sasa00770 | 
LOC106583705:  XM_014168218 sasa00471 | 
LOC100380852:  XM_014204667 sasa00770 | 
LOC106567123:  XM_014136048 sasa04514 |  XM_014136048 sasa04672 | 
LOC106566158:  XM_014134017 sasa00471 | 
LOC106583214:  XM_014167130 sasa04933 | 
LOC106565545:  XM_014132799 sasa04933 | 
LOC106575134:  XM_014151368 sasa04514 |  XM_014151368 sasa04512 |  XM_014151368 sasa04672 | 
LOC106608947:  XM_014207192 sasa04933 | 

Supplemental Files: 1065 genes in target file, of which 24 are implicated in pathways:

LOC106597439:  XM_014188636 sasa03050 | 
LOC106595251:  XM_014186627 sasa03050 | 
LOC106595599:  XM_014186964 sasa03050 | 
LOC106595602:  XM_014186967 sasa03050 | 
LOC106595421:  XM_014186794 sasa03050 | 
LOC106588562:  XM_014177695 sasa04512 |  XM_014177695 sasa04510 | 
LOC106581797:  XM_014164110 sasa00140 | 
LOC106567193:  XM_014136206 sasa03015 | 
LOC106607326:  XM_014204186 sasa04672 | 
LOC106570581:  XM_014143031 sasa04933 |  XM_014143031 sasa04672 | 
LOC106561972:  XM_014126469 sasa04933 | 
LOC106561972:  XM_014126470 sasa04933 | 
LOC106578082:  XM_014156667 sasa03015 | 
LOC106613117:  XM_014215067 sasa03050 | 
LOC106560399:  XM_014123279 sasa04933 |  XM_014123279 sasa04370 | 
LOC106560399:  XM_014123281 sasa04933 |  XM_014123281 sasa04370 | 
LOC106567123:  XM_014136048 sasa04672 | 
LOC106575086:  XM_014151267 sasa04510 | 
LOC106591920:  XM_014183188 sasa00100 | 
LOC106573007:  XM_014147603 sasa00100 | 
LOC106583214:  XM_014167130 sasa04933 | 
LOC106565545:  XM_014132799 sasa04933 | 
LOC106575134:  XM_014151368 sasa04512 |  XM_014151368 sasa04510 |  XM_014151368 sasa04672 | 
LOC106608947:  XM_014207192 sasa04933 |

731-3p (up-regulated)

Initial files: 1217 genes in target file of which 61 are implicated in pathways.

LOC106566983:  XM_014135702 sasa04933 | 
LOC106566983:  XM_014135703 sasa04933 | 
LOC106601422:  XM_014193629 sasa03015 | 
LOC106601422:  XM_014193630 sasa03015 | 
LOC106601423:  XM_014193632 sasa03015 | 
LOC106601423:  XM_014193633 sasa03015 | 
LOC106606965:  XM_014203472 sasa03015 | 
LOC106606965:  XM_014203473 sasa03015 | 
LOC106579762:  XM_014159927 sasa04933 | 
LOC106586398:  XM_014173631 sasa04512 | 
LOC106587420:  XM_014175797 sasa03015 | 
LOC106587420:  XR_001324442 sasa03015 | 
LOC106567445:  XM_014136708 sasa03015 | 
LOC106562230:  XM_014126959 sasa03015 | 
LOC106603879:  XM_014198090 sasa03015 | 
LOC106600761:  XM_014192376 sasa04933 | 
LOC106600761:  XM_014192377 sasa04933 | 
LOC106590686:  XM_014181846 sasa04933 | 
LOC106583949:  XM_014168656 sasa04933 | 
LOC106583949:  XM_014168657 sasa04933 | 
LOC106600761:  XM_014192378 sasa04933 | 
LOC106565094:  XM_014131780 sasa04514 | 
LOC106610502:  XM_014209886 sasa04933 |  XM_014209886 sasa04512 | 
LOC106565094:  XM_014131781 sasa04514 | 
LOC106588834:  XM_014178304 sasa04512 | 
LOC106572737:  XM_014147179 sasa04933 | 
LOC106585772:  XM_014172370 sasa04933 | 
LOC106572737:  XM_014147178 sasa04933 | 
LOC106579022:  XM_014158424 sasa03015 | 
LOC106562710:  XM_014127697 sasa00140 | 
LOC106560529:  XM_014123503 sasa04933 | 
LOC106607214:  XM_014203941 sasa04933 |  XM_014203941 sasa04514 | 
LOC106570589:  XM_014143042 sasa04514 |  XM_014143042 sasa04512 | 
LOC106590346:  XM_014181268 sasa04512 | 
LOC106574080:  XM_014149621 sasa04514 | 
LOC106565386:  XM_014132445 sasa03015 | 
LOC100136502:  XM_014163539 sasa04514 | 
LOC100136502:  XM_014163546 sasa04514 | 
LOC100136502:  XM_014163555 sasa04514 | 
LOC100136502:  XM_014163561 sasa04514 | 
LOC100136502:  XM_014163568 sasa04514 | 
LOC100136502:  XM_014163576 sasa04514 | 
LOC100136502:  XM_014163586 sasa04514 | 
LOC100136502:  XM_014163596 sasa04514 | 
LOC100136502:  XM_014163603 sasa04514 | 
LOC106588621:  XM_014177787 sasa04512 | 
LOC106588621:  XM_014177788 sasa04512 | 
LOC106571148:  XM_014143883 sasa04512 | 
LOC106570217:  XM_014142303 sasa04512 | 
LOC106570217:  XM_014142304 sasa04512 | 
LOC106609495:  XM_014208370 sasa04512 | 
LOC106589938:  XM_014180388 sasa00770 | 
LOC106589938:  XM_014180390 sasa00770 | 
LOC106598235:  XM_014189294 sasa04933 |  XM_014189294 sasa04512 | 
LOC106598235:  XM_014189295 sasa04933 |  XM_014189295 sasa04512 | 
LOC106588728:  XM_014178004 sasa04514 |  XM_014178004 sasa04512 | 
LOC106564737:  XM_014131047 sasa04512 | 
LOC106588794:  XM_014178221 sasa04514 |  XM_014178221 sasa04512 | 
LOC106598235:  XM_014189291 sasa04933 |  XM_014189291 sasa04512 | 
LOC106571148:  XM_014143881 sasa04512 | 
LOC106571148:  XM_014143882 sasa04512 | 

Supplementary files: 1112 genes in target file of which 72 implicated in pathways

LOC106566983:  XM_014135702 sasa04933 |  XM_014135702 sasa04370 | 
LOC106566983:  XM_014135703 sasa04933 |  XM_014135703 sasa04370 | 
LOC106601422:  XM_014193629 sasa03015 | 
LOC106601422:  XM_014193630 sasa03015 | 
LOC106601423:  XM_014193632 sasa03015 | 
LOC106601423:  XM_014193633 sasa03015 | 
LOC106606965:  XM_014203472 sasa03015 | 
LOC106606965:  XM_014203473 sasa03015 | 
LOC106579762:  XM_014159927 sasa04933 | 
LOC106586398:  XM_014173631 sasa04512 |  XM_014173631 sasa04510 | 
LOC106587420:  XM_014175797 sasa03015 | 
LOC106567445:  XM_014136708 sasa03015 | 
LOC106562230:  XM_014126959 sasa03015 | 
LOC106603879:  XM_014198090 sasa03015 | 
LOC106608064:  XM_014205744 sasa04510 | 
LOC106600761:  XM_014192376 sasa04933 | 
LOC106600761:  XM_014192377 sasa04933 | 
LOC106590686:  XM_014181846 sasa04933 | 
LOC106583949:  XM_014168656 sasa04933 | 
LOC106583949:  XM_014168657 sasa04933 | 
LOC106563223:  XM_014128592 sasa04510 | 
LOC106563223:  XM_014128596 sasa04510 | 
LOC106563223:  XM_014128597 sasa04510 | 
LOC106563223:  XM_014128599 sasa04510 | 
LOC106563223:  XM_014128600 sasa04510 | 
LOC106563223:  XM_014128601 sasa04510 | 
LOC106563223:  XM_014128590 sasa04510 | 
LOC106563223:  XM_014128591 sasa04510 | 
LOC106563223:  XM_014128593 sasa04510 | 
LOC106563223:  XM_014128594 sasa04510 | 
LOC106563223:  XM_014128595 sasa04510 | 
LOC106600761:  XM_014192378 sasa04933 | 
LOC106610502:  XM_014209886 sasa04512 |  XM_014209886 sasa04933 |  XM_014209886 sasa04510 | 
LOC106588834:  XM_014178304 sasa04512 |  XM_014178304 sasa04510 | 
LOC106565324:  XM_014132380 sasa04510 | 
LOC106565324:  XM_014132285 sasa04510 | 
LOC106565324:  XM_014132295 sasa04510 | 
LOC106565324:  XM_014132331 sasa04510 | 
LOC106565324:  XM_014132348 sasa04510 | 
LOC106565324:  XM_014132355 sasa04510 | 
LOC106565324:  XM_014132364 sasa04510 | 
LOC106565324:  XM_014132371 sasa04510 | 
LOC106565324:  XM_014132279 sasa04510 | 
LOC106565324:  XM_014132290 sasa04510 | 
LOC106565324:  XM_014132304 sasa04510 | 
LOC106565324:  XM_014132322 sasa04510 | 
LOC106565324:  XM_014132315 sasa04510 | 
LOC106565324:  XM_014132339 sasa04510 | 
LOC106572737:  XM_014147179 sasa04933 |  XM_014147179 sasa04370 | 
LOC106585772:  XM_014172370 sasa04933 |  XM_014172370 sasa04510 |  XM_014172370 sasa04370 | 
LOC106572737:  XM_014147178 sasa04933 |  XM_014147178 sasa04370 | 
LOC106579022:  XM_014158424 sasa03015 | 
LOC106562710:  XM_014127697 sasa00140 | 
LOC106560529:  XM_014123503 sasa04933 |  XM_014123503 sasa04510 |  XM_014123503 sasa04370 | 
LOC106607214:  XM_014203941 sasa04933 | 
LOC106570589:  XM_014143042 sasa04512 |  XM_014143042 sasa04510 | 
LOC106590346:  XM_014181268 sasa04512 |  XM_014181268 sasa04510 | 
LOC106565386:  XM_014132445 sasa03015 | 
LOC106588621:  XM_014177787 sasa04512 |  XM_014177787 sasa04510 | 
LOC106588621:  XM_014177788 sasa04512 |  XM_014177788 sasa04510 | 
LOC106571148:  XM_014143883 sasa04512 |  XM_014143883 sasa04510 | 
LOC106570217:  XM_014142303 sasa04512 |  XM_014142303 sasa04510 | 
LOC106570217:  XM_014142304 sasa04512 |  XM_014142304 sasa04510 | 
LOC106609495:  XM_014208370 sasa04512 | 
LOC106598235:  XM_014189294 sasa04512 |  XM_014189294 sasa04933 |  XM_014189294 sasa04510 | 
LOC106598235:  XM_014189295 sasa04512 |  XM_014189295 sasa04933 |  XM_014189295 sasa04510 | 
LOC106588728:  XM_014178004 sasa04512 |  XM_014178004 sasa04510 | 
LOC106564737:  XM_014131047 sasa04512 |  XM_014131047 sasa04510 | 
LOC106588794:  XM_014178221 sasa04512 |  XM_014178221 sasa04510 | 
LOC106598235:  XM_014189291 sasa04512 |  XM_014189291 sasa04933 |  XM_014189291 sasa04510 | 
LOC106571148:  XM_014143881 sasa04512 |  XM_014143881 sasa04510 | 
LOC106571148:  XM_014143882 sasa04512 |  XM_014143882 sasa04510 |