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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
SNX25P1	ENSG00000236809	-0.793135	2.94e-09	8.21e-05	0.333	0.679	Malignant cells	NA
RP11-474G23.3	NA	-0.797625	6.06e-08	1.69e-03	0.36	0.709	Malignant cells	NA
RP11-715J22.6	NA	-0.798097	2.17e-07	6.06e-03	0.493	0.761	Malignant cells	NA
CCDC96	ENSG00000173013	-0.799804	2.52e-08	7.04e-04	0.36	0.679	Malignant cells	NA
MT1L	ENSG00000260549	-0.800557	9.33e-09	2.61e-04	0.453	0.754	Malignant cells	NA
SYNGR4	ENSG00000105467	-0.801788	1.75e-08	4.89e-04	0.353	0.672	Malignant cells	NA
NPLOC4	ENSG00000182446	-0.804408	6.68e-07	1.87e-02	0.973	0.993	Malignant cells	NA
SGOL1	NA	-0.804836	3.78e-08	1.06e-03	0.713	0.948	Malignant cells	NA
RP4-604K5.3	NA	-0.806036	1.53e-06	4.27e-02	0.327	0.604	Malignant cells	NA
PLK1	ENSG00000166851	-0.810564	2.00e-08	5.60e-04	0.52	0.784	Malignant cells	NA
KIF14	ENSG00000118193	-0.81163	1.45e-08	4.05e-04	0.667	0.918	Malignant cells	NA
PSMC1	ENSG00000100764	-0.813257	7.46e-16	2.09e-11	0.987	1	Malignant cells	NA
TGM1	ENSG00000285348	-0.814226	3.76e-07	1.05e-02	0.173	0.455	Malignant cells	NA
CCNB2	ENSG00000157456	-0.814468	4.53e-10	1.27e-05	0.893	0.955	Malignant cells	NA
PA2G4	ENSG00000170515	-0.814515	1.61e-18	4.50e-14	1	0.993	Malignant cells	NA
BUB1B	ENSG00000156970	-0.81517	1.94e-09	5.43e-05	0.653	0.903	Malignant cells	NA
TXNL4A	ENSG00000141759	-0.81544	4.48e-17	1.25e-12	1	1	Malignant cells	NA
RP11-15E18.1	NA	-0.815733	7.35e-08	2.06e-03	0.427	0.761	Malignant cells	NA
NAA15	ENSG00000164134	-0.817353	4.38e-08	1.23e-03	0.96	1	Malignant cells	NA
NASP	ENSG00000132780	-0.817785	1.01e-15	2.83e-11	0.96	0.993	Malignant cells	NA
EEF1B2P3	ENSG00000232472	-0.81864	4.01e-07	1.12e-02	0.36	0.642	Malignant cells	NA
MRPS23	ENSG00000181610	-0.819043	4.34e-18	1.21e-13	1	1	Malignant cells	NA
ILF3	ENSG00000129351	-0.819538	3.92e-12	1.10e-07	1	1	Malignant cells	NA
NUDCD1	ENSG00000120526	-0.819954	1.01e-10	2.83e-06	0.98	0.985	Malignant cells	NA
RP11-689C9.1	NA	-0.820128	1.44e-06	4.01e-02	0.307	0.612	Malignant cells	NA
KIFC2	ENSG00000167702	-0.822142	9.02e-10	2.52e-05	0.387	0.746	Malignant cells	NA
LRPPRC	ENSG00000138095	-0.822202	2.16e-08	6.05e-04	0.993	0.993	Malignant cells	NA
TUBA1C	ENSG00000167553	-0.824496	5.47e-09	1.53e-04	1	0.993	Malignant cells	NA
AAK1	ENSG00000115977	-0.826348	1.73e-07	4.84e-03	1	0.993	Malignant cells	NA
SMARCD2	ENSG00000108604	-0.826703	9.88e-07	2.76e-02	0.853	0.933	Malignant cells	NA
SAR1A	ENSG00000079332	-0.829814	2.49e-17	6.96e-13	1	1	Malignant cells	NA
KRT8P39	ENSG00000233560	-0.831159	2.96e-08	8.28e-04	0.38	0.694	Malignant cells	NA
H2AFX	NA	-0.831733	8.93e-09	2.50e-04	0.933	0.985	Malignant cells	NA
DDX56	ENSG00000136271	-0.834647	8.39e-07	2.35e-02	0.96	0.993	Malignant cells	NA
DHX9	ENSG00000135829	-0.834655	3.37e-08	9.43e-04	0.987	1	Malignant cells	NA
RP11-551L14.4	NA	-0.836323	6.94e-07	1.94e-02	0.413	0.701	Malignant cells	NA
IMPDH2	ENSG00000178035	-0.837177	1.54e-13	4.31e-09	1	0.993	Malignant cells	NA
NOP58	ENSG00000055044	-0.838392	3.77e-18	1.05e-13	0.993	1	Malignant cells	NA
PRPF3	ENSG00000117360	-0.840042	1.81e-07	5.05e-03	0.927	0.955	Malignant cells	NA
RP11-496H1.1	NA	-0.840056	9.56e-07	2.67e-02	0.44	0.739	Malignant cells	NA
CTD-2139B15.1	NA	-0.840801	6.86e-08	1.92e-03	0.067	0.306	Malignant cells	NA
SUPT16H	ENSG00000092201	-0.841369	1.27e-18	3.55e-14	1	0.993	Malignant cells	NA
NSA2	ENSG00000164346	-0.844303	1.39e-07	3.88e-03	1	1	Malignant cells	NA
RAD51	ENSG00000051180	-0.849148	1.59e-06	4.46e-02	0.587	0.784	Malignant cells	NA
PLEKHN1	ENSG00000187583	-0.849942	1.41e-07	3.96e-03	0.427	0.739	Malignant cells	NA
CTC-260E6.6	NA	-0.852488	5.20e-09	1.46e-04	0.54	0.746	Malignant cells	NA
PRPF4B	ENSG00000112739	-0.854536	3.40e-07	9.51e-03	1	0.985	Malignant cells	NA
GDI2P2	ENSG00000233994	-0.854925	1.18e-07	3.30e-03	0.2	0.5	Malignant cells	NA
BRCA1	ENSG00000012048	-0.85559	6.61e-07	1.85e-02	0.627	0.881	Malignant cells	NA
DDX21	ENSG00000165732	-0.856826	9.01e-11	2.52e-06	1	1	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."