Difference between revisions of "MicroRNA and Salmo Salar"
| Line 148: | Line 148: | ||
Supplemental Files: | Supplemental Files: | ||
| − | 1065 genes in target file, of which | + | 1065 genes in target file, of which 24 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 | | ||
Revision as of 16:43, 26 January 2018
Contents
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 24 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 |
