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	Dataset summary
	Drug summary
	Umap of single cell types and conditions (resistant and sensitive)
	Comparison of cell composition between the resistant and sensitive groups (This dataset does not contain this module)
	Comparison of intra-tumor heterogeneity (ITH) and epithelial-mesenchymal transition (EMT) scores of malignant cells between the resistant and sensitive groups
	Difference of cell-cell interactions between the resistant and sensitive groups (This dataset does not contain this module)
	Differentially expressed genes (DEGs) between the resistant and sensitive groups for each cell type
	Mechanism analysis of drug resistance-related DEGs for each cell type in the pre-treatment samples (This dataset does not contain this module)
	Mechanism analysis of drug resistance-related DEGs for each cell type in the post-treatment samples (This dataset does not contain this module)
	Mechanism analysis of drug resistance-related DEGs for each cell type in one patient or cell lines
	MicroRNAs (miRNAs) regulating drug resistance-related DEGs for Malignant cells
	Motifs and transcription factors (TFs) regulating drug resistance-related DEGs for each cell type
•	Differentially expressed genes act as transcription factors

Dataset: GSE140440

Dataset summary for GSE140440

Datast information	Dataset	GSE140440
	PMID	32513898
	Raw data ID/link	PRJNA589746
	Organism	Homo sapiens
	Source	DU145 and PC cell lines
	Tissue	Cell line
	Cancer type level1	Prostate cancer
	Cancer type level2	Prostate cancer
	Regimen	docetaxel
	Drug type	Chemotherapy
	Sample size	resistant 2, sensitive 2
	Cell number	284
	Extract protocol	SMART-seq v4
	Data processing	NA
	Public date	Public on Sep 01, 2020
	Description	This dataset has 1 cell line with a sensitive pre-treatment sample and a resistant post-treatment sample.

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Drug summary for GSE140440

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"Docetaxel"	DB01248	small molecule	TUBB1; MAP2; MAP4; MAPT; BCL2; NR1I2	Q9H4B7; P11137; P27816; P10636; P10415; O75469

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Umap of single cell types and conditions (resistant and sensitive)

Umap of cell types and conditions (resistant and sensitive). If this dataset has both pre-treatment and post-treatment samples, the cell types were annotated together. If this dataset is a cell line dataset, the UMAP of cell clusters and the cell ratio of drug-resistant and sensitive groups within each cluster will also be shown. (If the image exists, the user can click on it to enlarge it in a new window.)

Umap of cell types	Umap of conditions
Umap of cell clusters	Cell ratio of drug-resistant and sensitive groups within each cluster

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Comparison of cell composition between the resistant and sensitive groups

In the pre-treatment samples, the cell composition of the resistant and sensitive groups were compared.
* represents significant difference. (If the image exists, the user can click on it to enlarge it in a new window.)

In the post-treatment samples, the cell composition of the resistant and sensitive groups were compared.
* represents significant difference. (If the image exists, the user can click on it to enlarge it in a new window.)

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Comparison of ITH and EMT scores of malignant cells between the resistant and sensitive groups

Comparison of ITH (intra-tumoral heterogeneity) and EMT (epithelial-mesenchymal transition) scores of malignant cells between the resistant and sensitive groups. ITH represents intratumoral heterogeneity, EMT represents epithelial mesenchymal transition, pre represents pre-treatment, post represents post-treatment, post2 represents longer post-treatment. (If the image exists, the user can click on it to enlarge it in a new window.)

Comparison of ITH scores

Comparison of EMT scores

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Difference of cell-cell interactions between the resistant and sensitive groups

In the pre-treatment samples, the difference in cell-cell interactions between the resistant and sensitive groups was compared. The numbers indicate the count of cell-cell interactions that were either higher or lower in the resistant group compared to the sensitive group. The dot plots of significant ligand-receptor pairs in the resistant group and sensitive group are subsequently displayed. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

In the post-treatment samples, the difference in cell-cell interactions between the resistant and sensitive groups was compared. The numbers indicate the count of cell-cell interactions that were either higher or lower in the resistant group compared to the sensitive group. The dot plots of significant ligand-receptor pairs in the resistant group and sensitive group are subsequently displayed. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

This dataset only has one patient or is a cell line dataset, the resistant sample is the post-treatment sample and the sensitive sample is the pre-treatment sample. The difference in cell-cell interactions between the resistant and sensitive groups was compared. The numbers indicate the count of cell-cell interactions that were either higher or lower in the resistant group compared to the sensitive group. The dot plots of significant ligand-receptor pairs in the resistant group and sensitive group are subsequently displayed. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

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Differentially expressed genes (DEGs) between the resistant and sensitive groups for each cell type

In the pre-treatment samples, the differentially expressed genes (|avg_log2FC|>0.25 & p_val_adj<0.05) between the resistant and sensitive groups for each cell type.

In the post-treatment samples, the differentially expressed genes (|avg_log2FC|>0.25 & p_val_adj<0.05) between the resistant and sensitive groups for each cell type.

This dataset only has one patient or is a cell line dataset, the resistant sample is the post-treatment sample and the sensitive sample is the pre-treatment sample. The following are differentially expressed genes (|avg_log2FC|>0.25 & p_val_adj<0.05) between the resistant and sensitive groups for each cell type.

Gene symbol	Gene id	avg_log2FC	p_val	p_val_adj	pct.1	pct.2	Cell type	Timepoint
TUBB4B	ENSG00000188229	-1.26577	1.96e-18	5.49e-14	1	1	Malignant cells	NA
ADRA1D	ENSG00000171873	-1.26652	6.73e-08	1.88e-03	0.373	0.694	Malignant cells	NA
ERCC6L	ENSG00000186871	-1.26828	3.17e-08	8.87e-04	0.46	0.799	Malignant cells	NA
DDX54	ENSG00000123064	-1.27448	4.77e-12	1.33e-07	0.827	0.993	Malignant cells	NA
PKP3	ENSG00000184363	-1.27544	1.78e-06	4.98e-02	0.347	0.612	Malignant cells	NA
HIST1H4J	NA	-1.27672	1.98e-12	5.54e-08	0.4	0.739	Malignant cells	NA
CDC6	ENSG00000094804	-1.28128	5.15e-09	1.44e-04	0.607	0.843	Malignant cells	NA
INF2	ENSG00000203485	-1.28234	7.03e-11	1.97e-06	0.707	0.963	Malignant cells	NA
MLEC	ENSG00000110917	-1.2852	1.32e-14	3.68e-10	1	1	Malignant cells	NA
ZNF544	ENSG00000198131	-1.28572	7.60e-13	2.12e-08	0.913	1	Malignant cells	NA
NCAPH	ENSG00000121152	-1.2873	7.84e-11	2.19e-06	0.433	0.806	Malignant cells	NA
VENTXP1	ENSG00000259849	-1.2894	3.54e-07	9.89e-03	0.053	0.269	Malignant cells	NA
CLSPN	ENSG00000092853	-1.29348	7.92e-17	2.22e-12	0.847	0.963	Malignant cells	NA
MISP	ENSG00000099812	-1.2981	5.72e-14	1.60e-09	0.26	0.761	Malignant cells	NA
LINC01521	ENSG00000213888	-1.30739	8.36e-07	2.34e-02	0.453	0.679	Malignant cells	NA
ADCY3	ENSG00000138031	-1.3076	4.44e-07	1.24e-02	0.547	0.754	Malignant cells	NA
MIR137HG	ENSG00000225206	-1.31033	2.81e-08	7.86e-04	0.287	0.597	Malignant cells	NA
ZNF714	ENSG00000160352	-1.3136	1.03e-09	2.88e-05	0.833	0.918	Malignant cells	NA
CEP131	ENSG00000141577	-1.31456	7.08e-10	1.98e-05	0.22	0.597	Malignant cells	NA
DIAPH1	ENSG00000131504	-1.31608	7.68e-08	2.15e-03	0.94	0.963	Malignant cells	NA
RP11-572O17.1	NA	-1.31666	7.38e-09	2.06e-04	0.373	0.716	Malignant cells	NA
BRIP1	ENSG00000136492	-1.31798	2.13e-08	5.94e-04	0.707	0.888	Malignant cells	NA
BOP1	ENSG00000285301	-1.31853	4.47e-14	1.25e-09	0.92	0.993	Malignant cells	NA
ZWINT	ENSG00000122952	-1.31903	7.20e-16	2.01e-11	0.933	1	Malignant cells	NA
SYNGR2	ENSG00000108639	-1.31947	3.23e-33	9.03e-29	1	1	Malignant cells	NA
ZNF670-ZNF695	ENSG00000135747	-1.33446	4.23e-07	1.18e-02	0.54	0.761	Malignant cells	NA
ZNF682	ENSG00000197124	-1.34352	1.04e-08	2.92e-04	0.34	0.642	Malignant cells	NA
TUBA1B	ENSG00000123416	-1.34377	3.05e-15	8.54e-11	0.993	1	Malignant cells	NA
NR2F6	ENSG00000160113	-1.34608	9.40e-08	2.63e-03	0.807	0.948	Malignant cells	NA
HSBP1L1	ENSG00000226742	-1.35043	8.12e-15	2.27e-10	0.713	0.97	Malignant cells	NA
ATAD3A	ENSG00000197785	-1.35088	3.19e-07	8.92e-03	0.687	0.843	Malignant cells	NA
MT-TV	ENSG00000210077	-1.35171	3.99e-13	1.12e-08	0.967	0.985	Malignant cells	NA
SPATA5	ENSG00000145375	-1.36	3.27e-07	9.13e-03	0.887	0.97	Malignant cells	NA
FTSJ3	ENSG00000108592	-1.3601	2.09e-10	5.83e-06	0.887	0.955	Malignant cells	NA
ZNF787	ENSG00000142409	-1.36421	1.56e-07	4.36e-03	0.48	0.716	Malignant cells	NA
LINC01224	ENSG00000269416	-1.36494	3.06e-10	8.57e-06	0.4	0.754	Malignant cells	NA
ZNF107	ENSG00000196247	-1.36529	5.91e-08	1.65e-03	0.373	0.657	Malignant cells	NA
ZNF486	ENSG00000256229	-1.37262	1.99e-10	5.57e-06	0.527	0.754	Malignant cells	NA
ROR1	ENSG00000185483	-1.37519	3.87e-07	1.08e-02	0.367	0.672	Malignant cells	NA
DMRT3	ENSG00000064218	-1.3815	5.33e-11	1.49e-06	0.14	0.485	Malignant cells	NA
CENPF	ENSG00000117724	-1.38179	1.04e-13	2.90e-09	0.913	1	Malignant cells	NA
RCC1	ENSG00000180198	-1.384	4.29e-11	1.20e-06	0.887	0.97	Malignant cells	NA
ANKRD30A	ENSG00000148513	-1.3893	5.31e-09	1.48e-04	0.267	0.59	Malignant cells	NA
JPH2	ENSG00000149596	-1.39212	2.93e-10	8.20e-06	0.347	0.687	Malignant cells	NA
CDC25A	ENSG00000164045	-1.39624	1.55e-08	4.33e-04	0.34	0.701	Malignant cells	NA
NRARP	ENSG00000198435	-1.40421	5.34e-07	1.49e-02	0.293	0.612	Malignant cells	NA
MESTIT1	ENSG00000272701	-1.40543	3.48e-08	9.72e-04	0.453	0.724	Malignant cells	NA
MRTO4	ENSG00000053372	-1.40645	4.81e-23	1.35e-18	0.987	1	Malignant cells	NA
MYCBP2	ENSG00000005810	-1.40713	1.75e-08	4.89e-04	0.92	0.97	Malignant cells	NA
HSPA1B	ENSG00000232804	-1.40853	7.15e-10	2.00e-05	0.887	0.993	Malignant cells	NA

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Mechanism analysis of drug resistance-related DEGs for each cell type in the pre-treatment samples

Enrichment results for 5 known drug-resistant mechanisms in malignant cells and 1 known mechanism in TME cells.The "Signature" column represents the differentially expressed genes (DEGs) used for enrichment. The "Geneset" column represents the genes included in this mechanism. The "Overlap" column represents the number of genes in the "Geneset" that are enriched in the "Signature". The "Enriched Genes" column represents the genes in the "Geneset" that are enriched in the "Signature". (If the image exists, the user can click on it to enlarge it in a new window.)

Hallmark, KEGG and GOBP enrichment results for up-regulated genes in resistant group of pre-treatment samples. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

Hallmark, KEGG and GOBP enrichment results for down-regulated genes in resistant group of pre-treatment samples. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window.Complete files can be downloaded from the download section.)

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Mechanism analysis of drug resistance-related DEGs for each cell type in the post-treatment samples

Enrichment results for 5 known drug resistance mechanisms in malignant cells and 1 known mechanism in TME cells.The "Signature" column represents the differentially expressed genes (DEGs) used for enrichment. The "Geneset" column represents the genes included in this mechanism. The "Overlap" column represents the number of genes in the "Geneset" that are enriched in the "Signature". The "Enriched Genes" column represents the genes in the "Geneset" that are enriched in the "Signature". (If the image exists, the user can click on it to enlarge it in a new window.)

Hallmark, KEGG and GOBP enrichment results for up-regulated genes in resistant group of post-treatment samples. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

Hallmark, KEGG and GOBP enrichment results for down-regulated genes in resistant group of post-treatment samples. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

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Mechanism analysis of drug resistance-related DEGs for each cell type in one patient or cell lines

This dataset only has one patient or is a cell line dataset, the resistant sample is the post-treatment sample and the sensitive sample is the pre-treatment sample. Enrichment results for 5 known drug resistance mechanisms in malignant cells and 1 known mechanism in TME cells are shown here.The "Signature" column represents the differentially expressed genes (DEGs) used for enrichment. The "Geneset" column represents the genes included in this mechanism. The "Overlap" column represents the number of genes in the "Geneset" that are enriched in the "Signature". The "Enriched Genes" column represents the genes in the "Geneset" that are enriched in the "Signature". (If the image exists, the user can click on it to enlarge it in a new window.)

Enrichment results for 5 known drug resistance mechanisms in malignant cells

Mechnism	Pval	FDR	Signature	Geneset	Overlap	Background	Cell type	Enriched Genes
Unusual Activation of Pro-survival Pathway	9.80e-06	4.90e-05	2352	781	116	23467	Malignant cells	ADAM9,ANXA2,AREG,BCAT1,BIRC5,BRCA1,CCND2,CDCP1,CDK6,CDKN1A,DNMT1,FAM168A,GSK3B,HOXA13,IGF2BP1,JUN,MAP1LC3B,PARP1,SOCS2,SPRY2,TGFB1,TGFBR2,PBK,TYMS,VEGFA,AAMDC,ADAM22,SLC25A5,AGR2,ANXA1,BCL10,BTG1,BUB1,CBL,CCNA2,CCNB1,CDK1,CCND1,CCNG2,CD44,HSPD1,CLTC,CLU,CUL4B,CYLD,DUSP2,DHFR,E2F2,ENG,ERCC1,ETS1,EZH2,FANCD2,FGFR1,FUS,FZD1,GPER1,GRB2,GCLM,SLC16A3,HMGB2,HMGN5,HSPA8,EIF4A3,IL1B,CXCL8,ING4,ITGA5,ITGB1,KIF11,KLF4,LDHA,MXD4,NF2,MYBL2,MYO10,NOTCH3,PARP8,PDCD4,PLK1,PSMB5,PTPN12,RAD51,RAB22A,RAB27A,RICTOR,RRM1,RRM2,ROCK2,SDC2,SMC4,SNAI2,SRI,STARD10,TERT,TFAM,TMEM54,TOP2B,USP14,USP22,PLAU,ERCC4,YEATS4,PFKFB3,GNAS,HMGCS1,INSIG1,ITGB3,PRKCA,RCN1,SQLE,SPHK1,GGPS1,SAFB2,PDSS1,ACAT2
Irregularity in Drug Uptake and Drug Efflux	1.60e-01	3.60e-01	2352	37	6	23467	Malignant cells	ABCB1,ABCC2,ABCA10,ABCF2,ABCE1,ABCG1
Drug Inactivation by Structure Modification	2.80e-01	3.60e-01	2352	27	4	23467	Malignant cells	GSS,NME1,CMPK1,CYP51A1
Aberration of the Drug's Therapeutic Target	2.90e-01	3.60e-01	2352	90	11	23467	Malignant cells	BRCA1,CDK6,DHFR,EZH2,FGFR1,IL1B,JAK1,COMT,DPP4,MAOA,TOP2A
Epigenetic Alteration of DNA, RNA or Protein	1.00e+00	1.00e+00	2352	455	20	23467	Malignant cells	DNMT1,GSK3B,H2AFY,HOXA13,EIF4G2,SPRY2,TYMS,EZH2,CXCL8,PDCD4,SMC4,TIMP1,SNHG1,LINC00261,GDI2,CDK14,CDR1,MX1,LINC00707,RP11-166P13.3

Hallmark, KEGG and GOBP enrichment results for up-regulated genes in resistant group. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

Up-regulated Hallmark	Up-regulated KEGG	Up-regulated GO BP

Hallmark, KEGG and GOBP enrichment results for down-regulated genes in resistant group. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

Down-regulated Hallmark	Down-regulated KEGG	Down-regulated GO BP

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MicroRNAs (miRNAs) regulating drug resistance-related DEGs for malignant cells

In the pre-treatment samples, the miRNAs with a score greater than 80 that regulate the top10 abs(avg_log2FC) drug resistance-related DEGs for malignant cells are shown here. If the gene does not have any miRNAs with a score greater than 80, it will not be shown. Here only the names of miRNAs with a score greater than 90 are shown, but some names will not be shown because of too many overlaps. (Complete files containing all datasets and cell types can be downloaded from the download section.)

In the post-treatment samples, the miRNAs with a score greater than 80 that regulate the top10 abs(avg_log2FC) drug resistance-related DEGs for Malignant cells are shown here. If the gene does not have any miRNAs with a score greater than 80, it will not be shown. Here only the names of miRNAs with a score greater than 90 are shown, but some names will not be shown because of too many overlaps. (Complete files containing all datasets and cell types can be downloaded from the download section.)

This dataset only has one patient or is a cell line dataset, the resistant sample is the post-treatment sample and the sensitive sample is the pre-treatment sample. The miRNAs with a score greater than 80 that regulate the top10 abs(avg_log2FC) drug resistance-related DEGs for Malignant cells are shown here. Here only the names of miRNAs with a score greater than 80 are shown, but some names will not be shown because of too many overlaps. If the gene does not have any miRNAs with a score greater than 90, it will not be shown. (Complete files containing all datasets and cell types can be downloaded from the download section.)

Regulating up-regulated DEGs in resistant group	Regulating down-regulated DEGs in resistant group

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Motifs and transcription factors (TFs) regulating drug resistance-related DEGs for each cell type

In the pre-treatment samples, the motifs and TFs that regulate drug resistance-related DEGs for each cell type are shown here. (Complete files can be downloaded from the download section.)

In the post-treatment samples, the motifs and TFs that regulate drug resistance-related DEGs for each cell type are shown here. (Complete files can be downloaded from the download section.)

This dataset only has one patient or is a cell line dataset, the resistant sample is the post-treatment sample and the sensitive sample is the pre-treatment sample. Motifs and TFs that regulate drug resistance-related DEGs for each cell type are shown here. (Complete files can be downloaded from the download section.)

Motifs and TFs regulating up-regulated DEGs in resistant group

motif

NES

AUC

TF_highConf

Cell_type

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Differentially expressed genes act as transcription factors

This table shows the differentially expressed genes that act as transcription factors. (Complete files can be downloaded from the download section.)

TF	motif	Expression	Cell type	Timepoint
KLF13	metacluster_195.2	up	Malignant cells	NA
KLF9	metacluster_195.2	up	Malignant cells	NA
KLF4	metacluster_195.2	up	Malignant cells	NA
KLF7	metacluster_195.2	up	Malignant cells	NA
KLF13	hocomoco__KLF13_HUMAN.H11MO.0.D	up	Malignant cells	NA
KLF13	transfac_pro__M07461	up	Malignant cells	NA
KLF4	transfac_pro__M07461	up	Malignant cells	NA
KLF7	transfac_pro__M07461	up	Malignant cells	NA
KLF9	transfac_pro__M07461	up	Malignant cells	NA
KLF7	metacluster_170.2	up	Malignant cells	NA

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1	"Sun X, Zhang Y, Li H, Zhou Y, Shi S, Chen Z, He X, Zhang H, Li F, Yin J, Mou M, Wang Y, Qiu Y, Zhu F. DRESIS: the first comprehensive landscape of drug resistance information. Nucleic Acids Res. 2023 Jan 6;51(D1):D1263-D1275. doi: 10.1093/nar/gkac812. PMID: 36243960; PMCID: PMC9825618."
2	"Wishart DS, Feunang YD, Guo AC, Lo EJ, Marcu A, Grant JR, Sajed T, Johnson D, Li C, Sayeeda Z, Assempour N, Iynkkaran I, Liu Y, Maciejewski A, Gale N, Wilson A, Chin L, Cummings R, Le D, Pon A, Knox C, Wilson M. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res. 2018 Jan 4;46(D1):D1074-D1082. doi: 10.1093/nar/gkx1037. PMID: 29126136; PMCID: PMC5753335."