Difference between revisions of "MicroRNA and Salmo Salar"

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Specific cells must be extracted from Excel files so that matching of data can occur between them.  
 
Specific cells must be extracted from Excel files so that matching of data can occur between them.  
−
* use Gumeric's ssconcvert to convert to TSV
+
* 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)
 
* 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
 
* use papath.py python script to match up genes implicated in pathways with the miRNA's target gene list

Revision as of 17:02, 26 January 2018

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:

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