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Xueqing edited this page Jan 16, 2018
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Stage 1 : Cleaned up the input data, got rid of low-quality ones and summed up the technical replicates. Mapped the transcripts to genes.
Stage 2 : Performed DESeq2 on the cleaned data to see the differential expression between each two adjacent disease stages. Filtered the results against protein-coding genes stored in HPA database. Filtered only the genes with FDR<=5% and analyzed the results.
Stage 3 : Performed Piano to enrich disturbed pathways in each progression stage of the disease. Filtered only the genes with FDR<=5% and analyzed the results, performed visualization. Two online enrichment tools, PathwAX and DAVID, are also tried and the results attached in the diary.
Alternative workflow performed by others :
ANOVA--Differential expression through all states, without differentiation of which progression status the changes belong to. The result of this part is not shown in the poster.