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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: GSE164897_Vem

Dataset summary for GSE164897_Vem

Datast information	Dataset	GSE164897_Vem
	PMID	34591417
	Raw data ID/link	PRJNA692421
	Organism	Homo sapiens
	Source	A375 cell line
	Tissue	Cell line
	Cancer type level1	Melanoma
	Cancer type level2	BRAFV600E-mutant melanoma
	Regimen	vemurafenib
	Drug type	Targeted therapy
	Sample size	resistant 1, sensitive 1
	Cell number	11008
	Extract protocol	10x genomics
	Data processing	CellRanger
	Public date	Public on Jan 16, 2021
	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 GSE164897_Vem

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"Vemurafenib"	DB08881	small molecule	BRAF	P15056

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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
DCBLD2	ENSG00000057019	0.288313	0.00e+00	0.00e+00	0.718	0.542	Malignant cells	NA
AMZ2	ENSG00000196704	0.287336	0.00e+00	0.00e+00	0.571	0.385	Malignant cells	NA
TPGS2	ENSG00000134779	0.286761	0.00e+00	0.00e+00	0.58	0.39	Malignant cells	NA
RNASEH2A	ENSG00000104889	0.285811	0.00e+00	0.00e+00	0.501	0.346	Malignant cells	NA
EBNA1BP2	ENSG00000117395	0.285377	0.00e+00	2.80e-45	0.695	0.589	Malignant cells	NA
PPARG	ENSG00000132170	0.285065	0.00e+00	0.00e+00	0.306	0.119	Malignant cells	NA
MKKS	ENSG00000125863	0.28407	0.00e+00	0.00e+00	0.744	0.603	Malignant cells	NA
IL1B	ENSG00000125538	0.283774	0.00e+00	0.00e+00	0.252	0.108	Malignant cells	NA
POP7	ENSG00000172336	0.283466	0.00e+00	0.00e+00	0.64	0.47	Malignant cells	NA
HMGA2	ENSG00000149948	0.283274	0.00e+00	0.00e+00	0.756	0.599	Malignant cells	NA
HAUS1	ENSG00000152240	0.282916	0.00e+00	0.00e+00	0.454	0.278	Malignant cells	NA
PFN2	ENSG00000070087	0.28273	0.00e+00	0.00e+00	0.673	0.5	Malignant cells	NA
RAD23A	ENSG00000179262	0.282524	0.00e+00	0.00e+00	0.918	0.858	Malignant cells	NA
SLC25A39	ENSG00000013306	0.281632	0.00e+00	0.00e+00	0.726	0.568	Malignant cells	NA
SMS	ENSG00000102172	0.281267	0.00e+00	0.00e+00	0.916	0.839	Malignant cells	NA
MANCR	ENSG00000231298	0.281111	0.00e+00	0.00e+00	0.316	0.124	Malignant cells	NA
H2AZ2	ENSG00000105968	0.279667	0.00e+00	0.00e+00	0.803	0.707	Malignant cells	NA
FLNA	ENSG00000196924	0.27816	0.00e+00	0.00e+00	0.632	0.446	Malignant cells	NA
NDUFB4	ENSG00000065518	0.277796	0.00e+00	0.00e+00	0.937	0.873	Malignant cells	NA
MMP24OS	ENSG00000126005	0.277704	0.00e+00	0.00e+00	0.411	0.248	Malignant cells	NA
TSPAN4	ENSG00000214063	0.277127	0.00e+00	0.00e+00	0.651	0.473	Malignant cells	NA
CLIC1	ENSG00000226651	0.275833	0.00e+00	0.00e+00	0.941	0.891	Malignant cells	NA
TMEM106C	ENSG00000134291	0.275625	0.00e+00	0.00e+00	0.608	0.448	Malignant cells	NA
PCBP1	ENSG00000169564	0.274246	0.00e+00	0.00e+00	0.727	0.568	Malignant cells	NA
SEC61G	ENSG00000132432	0.273981	0.00e+00	0.00e+00	0.993	0.972	Malignant cells	NA
METTL27	ENSG00000165171	0.273612	0.00e+00	0.00e+00	0.387	0.207	Malignant cells	NA
PSMD2	ENSG00000175166	0.273016	0.00e+00	0.00e+00	0.509	0.343	Malignant cells	NA
MAGOHB	ENSG00000111196	0.272326	0.00e+00	0.00e+00	0.489	0.329	Malignant cells	NA
GAMT	ENSG00000130005	0.272253	0.00e+00	0.00e+00	0.603	0.425	Malignant cells	NA
UBE2V2	ENSG00000169139	0.271799	0.00e+00	0.00e+00	0.661	0.522	Malignant cells	NA
GTF2H5	ENSG00000272047	0.271348	0.00e+00	0.00e+00	0.55	0.373	Malignant cells	NA
MRPL14	ENSG00000180992	0.270961	0.00e+00	0.00e+00	0.735	0.604	Malignant cells	NA
PSMB2	ENSG00000126067	0.270507	0.00e+00	0.00e+00	0.857	0.774	Malignant cells	NA
MYEOV	ENSG00000172927	0.269892	0.00e+00	0.00e+00	0.366	0.169	Malignant cells	NA
ALDH3B1	ENSG00000006534	0.268532	0.00e+00	0.00e+00	0.295	0.116	Malignant cells	NA
CAVIN1	ENSG00000177469	0.268382	0.00e+00	0.00e+00	0.512	0.321	Malignant cells	NA
C4orf3	ENSG00000164096	0.268292	0.00e+00	0.00e+00	0.569	0.424	Malignant cells	NA
DBI	ENSG00000155368	0.268239	0.00e+00	0.00e+00	0.796	0.683	Malignant cells	NA
HSPB11	ENSG00000081870	0.267816	0.00e+00	0.00e+00	0.62	0.467	Malignant cells	NA
RTL8A	ENSG00000203950	0.267573	0.00e+00	0.00e+00	0.589	0.419	Malignant cells	NA
HSPB1	ENSG00000106211	0.26544	0.00e+00	0.00e+00	0.993	0.981	Malignant cells	NA
SLC25A4	ENSG00000151729	0.26512	0.00e+00	0.00e+00	0.643	0.48	Malignant cells	NA
NBPF14	ENSG00000270629	0.263874	0.00e+00	0.00e+00	0.318	0.136	Malignant cells	NA
NDUFAF3	ENSG00000178057	0.263229	0.00e+00	0.00e+00	0.903	0.816	Malignant cells	NA
EEF2	ENSG00000167658	0.262291	0.00e+00	0.00e+00	0.997	0.993	Malignant cells	NA
MYOF	ENSG00000138119	0.262167	0.00e+00	0.00e+00	0.314	0.131	Malignant cells	NA
ABL2	ENSG00000143322	0.261979	0.00e+00	0.00e+00	0.409	0.241	Malignant cells	NA
VCL	ENSG00000035403	0.261229	0.00e+00	0.00e+00	0.354	0.177	Malignant cells	NA
TXNL4A	ENSG00000141759	0.261215	0.00e+00	0.00e+00	0.798	0.685	Malignant cells	NA
ACYP1	ENSG00000119640	0.260909	0.00e+00	0.00e+00	0.309	0.129	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	1.40e-14	7.10e-14	355	781	45	23467	Malignant cells	ANXA2,AREG,ATG12,BAX,BIK,CDKN1A,HMGA1,HMGA2,ID1,PKM,NFE2L2,NFKB1,PPARG,S100A4,STMN1,AKAP12,ANXA1,BAD,CAV2,CCN1,CCND1,HSPD1,DKK1,EPHA2,HMGB2,HSPB1,IL1B,IL24,LDHA,MAGEA3,NF2,NQO1,PGK1,ERBB3,S100A11,SOX10,UBE2C,AXL,YBX1,ENO1,GNAS,NPM1,EIF4EBP1,MDK,TRIB3
Aberration of the Drug's Therapeutic Target	1.60e-01	3.90e-01	355	90	3	23467	Malignant cells	IL1B,NPM1,AKR1B1
Epigenetic Alteration of DNA, RNA or Protein	5.40e-01	8.90e-01	355	455	7	23467	Malignant cells	BIK,LMNA,PPARG,PMAIP1,TIMP1,CYTOR,MALAT1
Drug Inactivation by Structure Modification	1.00e+00	1.00e+00	355	27	0	23467	Malignant cells
Irregularity in Drug Uptake and Drug Efflux	1.00e+00	1.00e+00	355	37	0	23467	Malignant cells

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	motif	NES	AUC	TF_highConf	Cell_type
	metacluster_137.2	5.58	0.0778	ATF3; BACH2; BATF; BATF; BATF; BATF; BATF3; FOS; FOS; FOS; FOS; FOS; FOS; FOS; FOS; FOS; FOS; FOSB; FOSB; FOSB; FOSB; FOSB; FOSL1; FOSL1; FOSL1; FOSL1; FOSL1; FOSL2; FOSL2; FOSL2; FOSL2; FOSL2; FOSL2; FOSL2; INSM2; JUN; JUN; JUN; JUN; JUN; JUN; JUN; JUN; JUN; JUN; JUN; JUN; JUNB; JUNB; JUNB; JUNB; JUNB; JUND; JUND; JUND; JUND; JUND; SMARCC1 (directAnnotation). ATF3; ATF3; BATF; FOS; FOSB; FOSL1; FOSL1; FOSL2; FOSL2; FOSL2; JUN; JUN; JUN; JUN; JUN; JUN; JUN; JUNB; JUND; JUND; JUND; JUND (inferredBy_Orthology).	Malignant cells
	metacluster_157.2	5.06	0.073	ATF3; ATF3; ATF3; BACH1; BACH1; BACH1; BACH2; BACH2; BACH2; BACH2; BATF; BATF; BCL11A; FOS; FOS; FOS; FOS; FOS; FOS; FOSB; FOSL1; FOSL1; FOSL1; FOSL1; FOSL1; FOSL1; FOSL2; FOSL2; FOSL2; JDP2; JDP2; JDP2; JDP2; JDP2; JDP2; JDP2; JUN; JUN; JUN; JUN; JUN; JUNB; JUNB; JUNB; JUNB; JUNB; JUNB; JUND; JUND; JUND; JUND; JUND; JUND; JUND; JUND; JUND; MAF; MAFB; MAFF; MAFG; MAFK; NFE2; NFE2; NFE2; NFE2; NFE2; NFE2; NFE2L1; NFE2L1; NFE2L2; NFE2L3; ZNF3; ZSCAN5C (directAnnotation). FOSL1; JUN; JUN; JUN; JUNB; JUNB; JUND (inferredBy_Orthology).	Malignant cells
	metacluster_22.34	4.21	0.0652	BACH2 (directAnnotation).	Malignant cells
	metacluster_74.23	3.96	0.063	HNF1B (inferredBy_Orthology).	Malignant cells
	tfdimers__MD00456	3.85	0.0619	E2F6; OVOL2 (directAnnotation).	Malignant cells
	metacluster_22.21	3.78	0.0613	NFE2L2 (inferredBy_Orthology).	Malignant cells
	metacluster_22.37	3.71	0.0607	BACH1 (directAnnotation).	Malignant cells
	tfdimers__MD00269	3.62	0.0598	CRX; PBX1 (directAnnotation).	Malignant cells
	metacluster_22.13	3.6	0.0596	MAFK (inferredBy_Orthology).	Malignant cells
	metacluster_74.5	3.54	0.0591	HNF1B (directAnnotation).	Malignant cells

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Motifs and TFs regulating down-regulated DEGs in resistant group

motif	motif	NES	AUC	TF_highConf	Cell_type
	taipale_tf_pairs__HOXB2_ETV1_ACCGGAAATGA_CAP	4.52	0.0984	ETV1; HOXB2 (directAnnotation).	Malignant cells
	transfac_pro__M06156	4.17	0.0931	ZNF75D (directAnnotation).	Malignant cells
	taipale_tf_pairs__MGA_DLX2_SYAATTANWGGTGYGA_CAP	4.13	0.0925	DLX2; MGA (directAnnotation).	Malignant cells
	taipale_tf_pairs__HOXB2_ETV4_ACCGGAAATGAN_CAP	4.05	0.0913	ETV4; HOXB2 (directAnnotation).	Malignant cells
	metacluster_141.4	3.99	0.0904	GLIS2 (directAnnotation).	Malignant cells
	tfdimers__MD00489	3.95	0.0897	IRF1; NR3C1 (directAnnotation).	Malignant cells
	transfac_pro__M05399	3.94	0.0896	SCRT2 (inferredBy_Orthology).	Malignant cells
	cisbp__M01816	3.88	0.0886	JUN (inferredBy_Orthology).	Malignant cells
	taipale_tf_pairs__ETV5_DLX2_RSCGGAANNNNNYAATTA_CAP	3.67	0.0853	DLX2; ETV5 (directAnnotation).	Malignant cells
	transfac_public__M00024	3.65	0.085	E2F1 (directAnnotation).	Malignant cells

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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
FOSL1	metacluster_137.2	up	Malignant cells	NA
FOSL1	metacluster_157.2	up	Malignant cells	NA
FOSL1	metacluster_50.1	up	Malignant cells	NA
SOX10	metacluster_153.3	down	Malignant cells	NA
NFE2L2	metacluster_157.2	down	Malignant cells	NA
NFE2L2	metacluster_22.21	down	Malignant cells	NA
NFE2L2	metacluster_22.32	down	Malignant cells	NA

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