Function enrichment for change max # transcript & predominant isoform

[sr320]

isoform done.......

still need list of genes in males and females where there was a change in max number of transcripts

[kubu4]

Females vs. Males:

https://github.com/sr320/ceabigr/blob/main/output/34-transcript-counts/diffs.max.transcripts_per_gene.females.vs.males.csv

Females Controls vs. Exposed:

https://github.com/sr320/ceabigr/blob/main/output/34-transcript-counts/diffs.max.transcripts_per_gene.controls_females.vs.exposed_females.csv

Males Controls vs. Exposed:

https://github.com/sr320/ceabigr/blob/main/output/34-transcript-counts/diffs.max.transcripts_per_gene.controls_males.vs.exposed_males.csv

These aren't the "final" lists. These still require filtering.

Here's the filtering method (genes are rows):

• If Column 3 < 0, Column 1 is < Column 2.
• If Column 3 > 0, Column 1 is > Column 2.

So, for the first file linked above (diffs.max.transcripts_per_gene.females.vs.males.csv), here's how the filtering criteria works:

• If Column 3 < 0, then males have higher number of max transcripts for a given gene.
• If Column 3 > 0, then females have a higher number of max transcripts for a given gene.

I can happily do the filtering an produce just the desired list(s). Just let me know.

EDITED: Fixed typo identified in this comment

[sr320]

At the end we want one table for males, one for females

x    Control MaxT #   Exposed MaxT #   Control Predom Isoform   Exposed Predome Isoform
Gene 1
Gene 2
Gene 3

[kubu4]

Yep, working on the combined table, per #93 .

[sr320]

If Column 3 < 0, then males have higher number of max transcripts for a given gene. If Column 3 < 0, then females have a higher number of max transcripts for a given gene.

????

Seems same?

[kubu4]

Seems same?

Yep, that's a typo.

Should be (If Column 3 > 0, then females have a higher number of max transcripts for a given gene.

Will edit previous post.

[kubu4]

But, basically, using the filename as a guide, it's always LEFT minus RIGHT. E.g.

diffs.max.transcripts_per_gene.females.vs.males.csv

This is comparing females.vs.males. So, the calculation is done FEMALES minus MALES.

Females will be Column 1 and males will be Column 2 in that file.

[sr320]

done. enrichment added to text for max transcripts (done irregardless of direction).

[yaaminiv]

@sr320 where's the code for the enrichment?

[yaaminiv]

Did functional enrichment with topGO for predominant isoforms.

• female sig BPGO: https://github.com/sr320/ceabigr/blob/main/output/42-predominant-isoform/fem-predIso-BP-FisherTestResults.csv
• female sig BPGO with gene annotations: https://github.com/sr320/ceabigr/blob/main/output/42-predominant-isoform/fem-predIso-BP-EnrichedGO-geneAnnot.csv
• male sig BPGO: https://github.com/sr320/ceabigr/blob/main/output/42-predominant-isoform/male-predIso-BP-FisherTestResults.csv
• male sig BPGO with gene annotations: https://github.com/sr320/ceabigr/blob/main/output/42-predominant-isoform/male-predIso-BP-EnrichedGO-geneAnnot.csv

Next step is examining methylation changes for genes with sig BPGO and repeating similar analysis for change in max transcripts

[yaaminiv]

Did functional enrichment wiht topGO for changes in the maximum transcript expressed

Females

• inc transcripts sig BPGO: https://github.com/sr320/ceabigr/blob/main/output/75-max-transcript-enrichment/fem-maxTransPos-BP-FisherTestResults.csv

• inc transcripts sig BPGO with gene annotation: https://github.com/sr320/ceabigr/blob/main/output/75-max-transcript-enrichment/fem-maxTransPos-BP-EnrichedGO-geneAnnot.csv

• dec transcripts sig BPGO: https://github.com/sr320/ceabigr/blob/main/output/75-max-transcript-enrichment/fem-maxTransNeg-BP-FisherTestResults.csv

• dec transcripts sig BPGO with gene annotation: https://github.com/sr320/ceabigr/blob/main/output/75-max-transcript-enrichment/fem-maxTransNeg-BP-EnrichedGO-geneAnnot.csv Males

• inc transcripts sig BPGO: https://github.com/sr320/ceabigr/blob/main/output/75-max-transcript-enrichment/male-maxTransPos-BP-FisherTestResults.csv

• inc transcripts sig BPGO with gene annotation: https://github.com/sr320/ceabigr/blob/main/output/75-max-transcript-enrichment/male-maxTransPos-BP-EnrichedGO-geneAnnot.csv

• dec transcripts sig BPGO: https://github.com/sr320/ceabigr/blob/main/output/75-max-transcript-enrichment/male-maxTransNeg-BP-FisherTestResults.csv

• dec transcripts sig BPGO with gene annotation: https://github.com/sr320/ceabigr/blob/main/output/75-max-transcript-enrichment/male-maxTransNeg-BP-EnrichedGO-geneAnnot.csv