Difference between revisions of "MicroRNA and Salmo Salar"
| Line 115: | Line 115: | ||
Initial files: | Initial files: | ||
1252 genes in target file, of which 3 implicated in pathways: | 1252 genes in target file, of which 3 implicated in pathways: | ||
| − | + | ||
| − | + | LOC106563775: XM_014129626 sasa04514 | |
| − | + | LOC106583677: XM_014168168 sasa03320 | |
| − | (LOC106583677 makes an appearance twice but once under alternative name XM_014168167 and XM_014168168) | + | LOC106583677: XM_014168167 sasa03320 |
| + | (LOC106583677 makes an appearance twice but as can be seen, it has a different once under alternative name XM_014168167 and XM_014168168) | ||
Supplemental Files: | Supplemental Files: | ||
1065 genes in target file, of which 5 implicated in pathways: | 1065 genes in target file, of which 5 implicated in pathways: | ||
| − | LOC106563775: sasa04514 | + | LOC106563775: XM_014129626 sasa04514 |
| − | LOC106596153: sasa04210 | + | LOC106596153: XM_014187472 sasa04210 |
| − | LOC106574656: sasa04060 | + | LOC106574656: XM_014150653 sasa04060 |
| − | LOC106582588: sasa04210 | + | LOC106582588: XM_014165814 sasa04210 |
| − | LOC106575727: sasa04060 | + | LOC106575727: XM_014152386 sasa04060 |
Revision as of 16:17, 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
Initial files: 1252 genes in target file, of which 3 implicated in pathways:
LOC106563775: XM_014129626 sasa04514 LOC106583677: XM_014168168 sasa03320 LOC106583677: XM_014168167 sasa03320 (LOC106583677 makes an appearance twice but as can be seen, it has a different once under alternative name XM_014168167 and XM_014168168)
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
