Publication results

EMT experiment

DE-kupl was run using RNA-seq libraries from Yang et al.(1) retrieved on the GEO web site under accession GSE75492.

Samples

The following Fastq files were used:

SRA_id condition timepoint replicate number
GSM1956974 E No Dox rep1
GSM1956975 E No Dox rep2
GSM1956976 E No Dox rep3
GSM1956977 E Day1 rep1
GSM1956978 E Day1 rep2
GSM1956979 E Day1 rep3
GSM1956992 M Day6 rep1
GSM1956993 M Day6  rep2
GSM1956994 M Day6 rep3
GSM1956995 M Day7 rep1
GSM1956996 M Day7 rep2
GSM1956997 M Day7 rep3

DE-kupl Parameters

DE-kupl was executed with the following parameters:

  • min_recurrence: 6
  • min_recurrence_abundance: 5
  • pvalue_threshold: 0.05
  • lib_type: stranded
  • diff_method: ttest
  • conditions: E vs M

Output files

These output files are availabe for download:

Filename Description
DiffContigsInfos.tsv.gz Contig table
diff_contigs.bed.gz Contig bed file (Human HG38 coordinates)
ContigsPerLoci.tsv.gz Locus table

References

(1) Yang Y. et al (2016) Determination of a Comprehensive Alternative Splicing Regulatory Network and Combinatorial Regulation by Key Factors during the Epithelial-to-Mesenchymal Transition. Mol Cell Biol 36:1704-19.

GTEx / HPA Cross validation data

Output files

Filename Description
libraries.txt Description of GTEx and HPA libraries used.
DiffContigsInfos.tsv.gz Result of DEkupl run on GTEx data: contig table
diff_contigs.bed.gz Result of DEkupl run on GTEx data: contig bed file (Human HG38 coordinates)
gtex.fa Fasta file with selection of representative k-mers for best contigs (higher abs(fold change)) in each category :
  • polyA (100)
  • splice (100)
  • lincRNA (100)
  • intron_DU (100)
  • repeat (100)
  • unmapped (50)
For each k-mer, the fasta comment line contains: [event class] [contig #] [mean count Colon] [mean cout Skin] [up or down in Skin]