MicroRNA and Salmo Salar

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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

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 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 5 implicated in pathways: 

LOC106563775:  XM_014129626 sasa04514 
LOC106596153:  XM_014187472 sasa04210 
LOC106574656:  XM_014150653 sasa04060 
LOC106582588:  XM_014165814 sasa04210 
LOC106575727:  XM_014152386 sasa04060
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