ת¼ô࣬ôôҵоʲôϵ
Ӵ̵Ǹ
Сש~
Part1 ʿ
1.1ʿ
ʧйأܲԼԼȶصӰ ɴ¼άȾв1ںIJclean bases>6Gôok֪Ҫ Ҫпɱлںϻû⣬Ӳ⼴ɣ 2ֵQ20/Q30ٷֱȣQ20/Q30>85%-90% ˵ DzͼֵкʿҪͿԶĵ¿~
1.2οȶ
ֻעͽã//Сȣοȶʣtotal mappedһƽҪ>85% >85%Ļȶֲreads 85%ڸ֣˵Ϣ ǷֻͨעͲôôȶҪͻʵһЩأ>60-85%λƾ֤ξۺжϹ
1.3ѧظ
ʵƣ飩 Case vs Control ó/ vs ȣ2ѧmRNAǷϵPCAṩյ
1ϵԽ1ע֮ģʽƶԽߣ ͳһѧظԭ˵A1/A2/A3/A4/A5…ϵԽ˵ͬڵѧظԽã AB飩֮ϵԽԽã˵֮IJԽIJԽࣻ
2ͬͳһԽ˵ѧظԽã PCAоԽԶԽã˵Խ ȻϵPCA⣬Ҫ죬ڴȲ~
Part2ɸѡ/ѡЧӻ
2.1ɸѡ/ѡ
ĬϽpadjС0.05|log2(foldchange)| 1Ϊɸѡı±ɷЩ2бת䣨ϵµЩתпܺʹóͷ/أΪоĺѡ
ɸѡIJܽôͨFoldChangepadj/pԽСԽãڸбΣFPKMЧעЩؾнһɸ ԽһСѡģ Dz٣֮ſɸѡʹĻ ȻʵɸѡУʵĿξиԻ~
2.2 /ѡӻչʾ
ɸѡ/ѡ10-100ڣǶЩпӻչʾͼɽͼPPIͼ~
ͼչʾڸ/еıΣɫԽԽߣ ɽͼչʾ/ѡIJΣ PPI·ͼչʾЩ֮AԽ࣬˵以ĻԽ࣬A/ܵصĻԽ࣬AÿԽҪ
Part3ЧЧӻ
3.1 Ч
GO/KEGGɢͼǸЧһֿӻչʾ Ĭѡ Top20 GO term/pathwayչʾͼͨRich factorP value Gene number (ͨ·ϵĻ)Ȩ主ˮƽ Ȼע/ȤGO term/pathwayҲĿterm иԻ⣬ʵֶضЧľ۽
3.2 GSEA
GSEA עijﱬıĻضЧеıһԣԴ̺ѧϢ GSEAֵֹɸѡ ͼͼҪͨNESP/FDR (ԣԽСԽ)Ȩ主ˮƽ NESֵࣨA飩Ը˵term Aдڼ״̬֮Bд״̬ NESֵҲࣨB飩Ը˵term Bдڼ״̬ ע/ȤGO term/pathwayԵչʾ主ι~
Part4Ի
4.1
ΪݶµĽ㣬ʵƣ3-5飩漰ݶȴóͷʱת䡢ҩŨ/ת䡢ˮƽڵȣʹ/ʱģʽƵĻй࣬ӶҵʵתдԵĻӦclusterչתеļ ɸѡԤڱкϵclusterԶضclusterлЧȣ
4.2 WGCNA
WGCNAWeighted Gene Co-expression Network analysisȨ WGCNA൱ڶԶشѰ/͵飬Ӷһ(ԶڻGO/KEGGPPIȵ)
Tips:ѯϸЧڹ/ͬԻȣӴʱϵUGĿϻСͬ~
