gse121212

repo for reproducing gse121212 study

Links

The publication: Atopic Dermatitis Is an IL-13–Dominant Disease with Greater Molecular Heterogeneity Compared to Psoriasis

Raw data repository: SRA Run Selector

AD Data

No.	Type	Comparision	Read R object
1	DGE list	aLSvsCO (acute lesion vs healthy control)	readRDS(url("https://rawcdn.githack.com/tuhulab/gse121212/ab5db865c53d44ee381294bbaec34c31013e1f52/data/rds/aLS_CO_DGE.rds"))
2	DGE list	aLSvsNL (acute lesion vs non-lesion (subject matched)	readRDS(url("https://rawcdn.githack.com/tuhulab/gse121212/ab5db865c53d44ee381294bbaec34c31013e1f52/data/rds/aLS_NL_DGE.rds"))
3	DGE list	cLSvsCO (chronic lesion vs healthy control)	readRDS(url("https://rawcdn.githack.com/tuhulab/gse121212/ab5db865c53d44ee381294bbaec34c31013e1f52/data/rds/cLS_CO_DGE.rds"))
4	DGE list	cLSvsNL (chronic lesion vs non-lesion (subject matched)	readRDS(url("https://rawcdn.githack.com/tuhulab/gse121212/ab5db865c53d44ee381294bbaec34c31013e1f52/data/rds/cLS_NL_DGE.rds"))
5	DGE list	NLvsCO (non-lesion vs healthy control)	readRDS(url("https://rawcdn.githack.com/tuhulab/gse121212/ab5db865c53d44ee381294bbaec34c31013e1f52/data/rds/NL_CO_DGE.rds"))
6	data list	raw counts (filtering out lowly expressed genes)	readRDS(url("https://rawcdn.githack.com/tuhulab/gse121212/9d921a28370fe4c2222e02722cde59f61e8d4f51/data/rds/gse121212_list_raw.rds"))
1*	DGE list	aLSvsCO_all (acute lesion vs healthy control, all genes)	readRDS(url("https://rawcdn.githack.com/tuhulab/gse121212/13d9d300bfd98adc70f85315eab7d7d619bad3bc/data/rds/aLS_CO_DGE_all.rds"))
2*	DGE list	aLSvsNL_all (acute lesion vs non-lesion (subject matched, all genes)	readRDS(url("https://rawcdn.githack.com/tuhulab/gse121212/9e4484a64028b51d987d6157ba0112b48c0f7323/data/rds/aLS_NL_DGE_all.rds"))
3*	DGE list	cLSvsCO_all (chronic lesion vs healthy control, all genes)	readRDS(url("https://rawcdn.githack.com/tuhulab/gse121212/13d9d300bfd98adc70f85315eab7d7d619bad3bc/data/rds/cLS_CO_DGE_all.rds"))
4*	DGE list	cLSvsNL_all (chronic lesion vs non-lesion (subject matched, all genes)	readRDS(url("https://rawcdn.githack.com/tuhulab/gse121212/fa5ca19185fdb4c429a03e61c2b0f495c8e5fd23/data/rds/cLS_NL_DGE.rds"))
5*	DGE list	NLvsCO (non-lesion vs healthy control, all genes)	readRDS(url("https://rawcdn.githack.com/tuhulab/gse121212/13d9d300bfd98adc70f85315eab7d7d619bad3bc/data/rds/NL_CO_DGE_all.rds"))

1-5: AD Differentially expressed genes (|log2FC|>1, adj. p<0.05); aLS - acute lesion; CO - healthy control; cLS - chronic lesion; NL - non-lesional 6: raw counts, metadata, gene annotation 1*-5*: AD (all genes)

PSO data

no	list	command
1	DGE list (including all genes) - PSO LS vs NL, subject matched	readRDS(url("https://rawcdn.githack.com/tuhulab/gse121212/3d41fde27376cf24a6cea12f90af4a6de4c9e162/data/rds/PSO/PSO_LS_NL_DGE_all.rds"))
2	DGE list (including all genes) - PSO LS vs CO	readRDS(url("https://rawcdn.githack.com/tuhulab/gse121212/3d41fde27376cf24a6cea12f90af4a6de4c9e162/data/rds/PSO/PSO_LS_CO_DGE_all.rds"))
3	DGE list (including all genes) - PSO NL vs CO	readRDS(url("https://rawcdn.githack.com/tuhulab/gse121212/3d41fde27376cf24a6cea12f90af4a6de4c9e162/data/rds/PSO/PSO_NL_CO_DGE_all.rds"))

Materials and methods

Bioinformatics tools

Generaly Applicable Gene-set Enrichment for Pathway Analysis (GAGE)

Enrichr