Q1: there are various time points between control and treatment. Should we use the consensus DEG list?
IN the BGI report go to /Differential.../DEGList/
(There is an R package NOISeq)
BGI already did the analysis, we need to do a better job @11,12
check NOISeq in the report page 16/23-17/23-...
do a good job on that parts for a manuscript:
11-Pathway Analysis of DEG: functional enrichment phyer, hypergeormetric_distribution
12- PPI Analysis of DEG
It seems "GeneID" in BGI report are from NCBI. Example GeneID: 57573 is a standard ID.
1)b-Pathway analysis plan for DE gene lists
TODO: There are different sources of human gene/protein networks. We should try several for comparisons
TODO: We should try different clustering method, such as hlcust, mcl, etc (refer to Qin's previous paper for clustering analysis).
2)a-time-lapsed image analysis for yeast replicative lifespan
softwares:ImageJ, MATLAB, R
https://www.mendeley.com/groups/ gene -pathways/ pathway analysis
gene set analysis is a basic thing, we also need to do that.
data visualization course would be good for animations of .gifs
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