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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
EPHA2	ENSG00000142627	0.543531	0.00e+00	0.00e+00	0.549	0.207	Malignant cells	NA
AXL	ENSG00000167601	0.540532	0.00e+00	0.00e+00	0.708	0.466	Malignant cells	NA
GPRC5A	ENSG00000013588	0.538213	0.00e+00	0.00e+00	0.699	0.458	Malignant cells	NA
FHL2	ENSG00000115641	0.537195	0.00e+00	0.00e+00	0.599	0.35	Malignant cells	NA
BAX	ENSG00000087088	0.528657	0.00e+00	0.00e+00	0.792	0.575	Malignant cells	NA
MIR4435-2HG	ENSG00000172965	0.527462	0.00e+00	0.00e+00	0.625	0.31	Malignant cells	NA
CCND1	ENSG00000110092	0.52664	0.00e+00	0.00e+00	0.896	0.775	Malignant cells	NA
PDLIM1	ENSG00000107438	0.5166	0.00e+00	0.00e+00	0.578	0.276	Malignant cells	NA
CAPN2	ENSG00000162909	0.513644	0.00e+00	0.00e+00	0.672	0.366	Malignant cells	NA
ACTB	ENSG00000075624	0.501433	0.00e+00	0.00e+00	0.999	0.999	Malignant cells	NA
CCN1	ENSG00000142871	0.498215	0.00e+00	0.00e+00	0.427	0.172	Malignant cells	NA
GAGE1	ENSG00000205777	0.497402	0.00e+00	0.00e+00	0.423	0.106	Malignant cells	NA
SNRPG	ENSG00000143977	0.491098	0.00e+00	0.00e+00	0.987	0.985	Malignant cells	NA
GADD45A	ENSG00000116717	0.478741	1.82e-44	2.80e-40	0.547	0.415	Malignant cells	NA
THBS1	ENSG00000137801	0.477664	0.00e+00	0.00e+00	0.464	0.188	Malignant cells	NA
NPC2	ENSG00000119655	0.474828	0.00e+00	0.00e+00	0.93	0.779	Malignant cells	NA
SNAPC1	ENSG00000023608	0.473803	0.00e+00	0.00e+00	0.437	0.244	Malignant cells	NA
APOBEC3G	ENSG00000239713	0.469306	0.00e+00	0.00e+00	0.36	0.109	Malignant cells	NA
PTTG1	ENSG00000164611	0.46456	0.00e+00	0.00e+00	0.734	0.581	Malignant cells	NA
C12orf75	ENSG00000235162	0.45965	0.00e+00	0.00e+00	0.679	0.41	Malignant cells	NA
UBE2C	ENSG00000175063	0.451401	0.00e+00	0.00e+00	0.46	0.316	Malignant cells	NA
DDB2	ENSG00000134574	0.447593	0.00e+00	0.00e+00	0.43	0.207	Malignant cells	NA
TXN	ENSG00000136810	0.443465	0.00e+00	0.00e+00	1	0.999	Malignant cells	NA
ANXA2	ENSG00000182718	0.442635	0.00e+00	0.00e+00	0.918	0.978	Malignant cells	NA
FTH1	ENSG00000167996	0.442543	0.00e+00	0.00e+00	1	1	Malignant cells	NA
ANPEP	ENSG00000166825	0.441413	0.00e+00	0.00e+00	0.5	0.218	Malignant cells	NA
UBE2T	ENSG00000077152	0.44138	0.00e+00	0.00e+00	0.478	0.278	Malignant cells	NA
SUB1	ENSG00000113387	0.438968	0.00e+00	0.00e+00	0.963	0.886	Malignant cells	NA
ANXA1	ENSG00000135046	0.437267	0.00e+00	0.00e+00	0.868	0.721	Malignant cells	NA
PLAUR	ENSG00000011422	0.436733	0.00e+00	0.00e+00	0.543	0.287	Malignant cells	NA
CD9	ENSG00000010278	0.426167	0.00e+00	0.00e+00	0.61	0.35	Malignant cells	NA
RPA3	ENSG00000106399	0.424296	0.00e+00	0.00e+00	0.739	0.591	Malignant cells	NA
C4orf48	ENSG00000243449	0.424071	0.00e+00	0.00e+00	0.717	0.475	Malignant cells	NA
CDC20	ENSG00000117399	0.423004	0.00e+00	0.00e+00	0.479	0.29	Malignant cells	NA
LY6K	ENSG00000160886	0.418893	0.00e+00	0.00e+00	0.69	0.508	Malignant cells	NA
UBE2S	ENSG00000108106	0.418858	0.00e+00	0.00e+00	0.9	0.862	Malignant cells	NA
ALDOA	ENSG00000149925	0.416074	0.00e+00	0.00e+00	1	0.999	Malignant cells	NA
RHEB	ENSG00000106615	0.414171	0.00e+00	0.00e+00	0.796	0.639	Malignant cells	NA
H1-2	ENSG00000187837	0.413897	2.35e-39	3.72e-35	0.405	0.295	Malignant cells	NA
CSTB	ENSG00000160213	0.410073	0.00e+00	0.00e+00	0.899	0.776	Malignant cells	NA
PLK2	ENSG00000145632	0.409111	0.00e+00	0.00e+00	0.432	0.204	Malignant cells	NA
DRAP1	ENSG00000175550	0.408605	0.00e+00	0.00e+00	0.963	0.899	Malignant cells	NA
SCG5	ENSG00000277614	0.408012	0.00e+00	0.00e+00	0.512	0.279	Malignant cells	NA
SLC9A3R2	ENSG00000065054	0.406371	0.00e+00	0.00e+00	0.47	0.216	Malignant cells	NA
PGK1	ENSG00000102144	0.405623	0.00e+00	0.00e+00	0.89	0.832	Malignant cells	NA
PLAT	ENSG00000104368	0.404907	0.00e+00	0.00e+00	0.36	0.137	Malignant cells	NA
TMSB10	ENSG00000034510	0.403232	0.00e+00	0.00e+00	1	1	Malignant cells	NA
CKS1B	ENSG00000173207	0.398107	0.00e+00	0.00e+00	0.784	0.706	Malignant cells	NA
BIK	ENSG00000100290	0.3966	0.00e+00	0.00e+00	0.322	0.074	Malignant cells	NA
COX17	ENSG00000138495	0.39494	0.00e+00	0.00e+00	0.981	0.937	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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