diff --git a/README.md b/README.md index 564ef0c6cea11ca0bd1d0808c60d37fa58b42717..a4a6cfdde2b337b1cda58826e52daa00db1c616b 100644 --- a/README.md +++ b/README.md @@ -34,15 +34,15 @@ Determining cellular heterogeneity in the human prostate with single-cell RNA se * Genesets * "regev\_lab\_cell\_cycle\_genes.txt" G2M and S phase genes from [*Genome Res. 2015 Dec; 25(12): 1860–1872*](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4665007/) - * "DEG\_C2.CGP.M10970.txt" MSigDB C2 Chemical and Genetic Perturbations M10970 **CHUANG\_OXIDATIVE\_STRESS\_RESPONSE\_UP** + * "DEG\_C2.CGP.M10970.txt" MSigDB C2 Chemical and Genetic Perturbations M10970 [**CHUANG\_OXIDATIVE\_STRESS\_RESPONSE\_UP**](http://software.broadinstitute.org/gsea/msigdb/cards/CHUANG_OXIDATIVE_STRESS_RESPONSE_UP.html) * "DEG\_Epi_2FC.txt" DWS generated DEGs of Epithelia from FACS population (bulk) RNA-sequencing * "DEG\_FMSt_2FC.txt" DWS generated DEGs of Fibromuscular Stroma from FACS population (bulk) RNA-sequencing * "DEG\_BE_2FC.txt" DWS generated DEGs of Basal Epithelia from FACS population (bulk) RNA-sequencing * "DEG\_LE_2FC.txt" DWS generated DEGs of Luminal Epithelia from FACS population (bulk) RNA-sequencing * "DEG\_OE_2FC.txt" DWS generated DEGs of "Other" Epithelia from FACS population (bulk) RNA-sequencing - * "DEG\_C5.BP.M11704.txt" MSigDB C5 GO Biological Processes M11704 **GO\_CELL\_DIFFERENTIATION** - * "DEG\_C5.BP.M10794.txt" MSigDB C5 GO Biological Processes M10794 **GO\_SMOOTH\_MUSCLE\_CELL\_DIFFERENTIATION** - * "DEG\_C5.BP.M13024.txt" MSigDB C5 GO Biological Processes M13024 **GO\_REGULATION\_OF\_FIBROBLAST\_PROLIFERATION** + * "DEG\_C5.BP.M11704.txt" MSigDB C5 GO Biological Processes M11704 [**GO\_ENDOTHELIAL\_CELL\_DIFFERENTIATION**](http://software.broadinstitute.org/gsea/msigdb/cards/GO_ENDOTHELIAL_CELL_DIFFERENTIATION.html) + * "DEG\_C5.BP.M10794.txt" MSigDB C5 GO Biological Processes M10794 [**GO\_SMOOTH\_MUSCLE\_CELL\_DIFFERENTIATION**](http://software.broadinstitute.org/gsea/msigdb/cards/GO_SMOOTH_MUSCLE_CELL_DIFFERENTIATION.html) + * "DEG\_C5.BP.M13024.txt" MSigDB C5 GO Biological Processes M13024 [**GO\_REGULATION\_OF\_FIBROBLAST\_PROLIFERATION**](http://software.broadinstitute.org/gsea/msigdb/cards/GO_REGULATION_OF_FIBROBLAST_PROLIFERATION.html) * "EurUrol.2005.NE.txt" Neuroendocrine markers from Table 1 of [*Eur Urol. 2005 Feb;47(2):147-55*](https://www.ncbi.nlm.nih.gov/pubmed/15661408) * "Basal cells-signature-genes.csv" scRNA-Sequencing Lung Map generated top 20 DEGs for human lung Basal Cells * "Normal AT2 cells-signature-genes.csv" scRNA-Sequecing Lung Map generated top 20 DEGs for human lung Alveolar Type 2 Cells @@ -53,5 +53,5 @@ Determining cellular heterogeneity in the human prostate with single-cell RNA se * Pericytes, Matrix Fibroblasts * Endothelial Cells * Myeloid/Immune Cells - * "DWS.scStress.txt DWS generated DEGs of Stressed Cells from scRNA-Sequencing - * "DWS.scNE.txt DWS generated DEGs of Neuroendocrine Cells from scRNA-Sequencing + * "DWS.scStress.txt" DWS generated DEGs of Stressed Cells from scRNA-Sequencing + * "DWS.scNE.txt" DWS generated DEGs of Neuroendocrine Cells from scRNA-Sequencing