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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_VemCob

Dataset summary for GSE164897_VemCob

Datast information	Dataset	GSE164897_VemCob
	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 + combimetinib
	Drug type	Targeted therapy
	Sample size	resistant 1, sensitive 1
	Cell number	14851
	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_VemCob

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"Vemurafenib"	DB08881	small molecule	BRAF	P15056
"combimetinib" is not included in the drug list.

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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
CYTOR	ENSG00000222041	0.544756	0.00e+00	0.00e+00	0.524	0.313	Malignant cells	NA
FOXD1	ENSG00000251493	0.544213	0.00e+00	0.00e+00	0.311	0.039	Malignant cells	NA
TXNRD1	ENSG00000198431	0.542084	0.00e+00	0.00e+00	0.418	0.172	Malignant cells	NA
BANF1	ENSG00000175334	0.541965	0.00e+00	0.00e+00	0.83	0.713	Malignant cells	NA
CD68	ENSG00000129226	0.540559	0.00e+00	0.00e+00	0.451	0.213	Malignant cells	NA
PRRC2C	ENSG00000117523	0.539118	0.00e+00	0.00e+00	0.684	0.56	Malignant cells	NA
SNRPD1	ENSG00000167088	0.533932	0.00e+00	0.00e+00	0.955	0.881	Malignant cells	NA
ENY2	ENSG00000120533	0.530001	0.00e+00	0.00e+00	0.756	0.641	Malignant cells	NA
DDX5	ENSG00000108654	0.527609	0.00e+00	0.00e+00	0.783	0.672	Malignant cells	NA
TIMM10	ENSG00000134809	0.526175	0.00e+00	0.00e+00	0.5	0.312	Malignant cells	NA
UQCRH	ENSG00000173660	0.525394	0.00e+00	0.00e+00	1	1	Malignant cells	NA
PPIB	ENSG00000166794	0.525284	0.00e+00	0.00e+00	0.893	0.841	Malignant cells	NA
HNRNPAB	ENSG00000197451	0.525154	0.00e+00	0.00e+00	0.523	0.351	Malignant cells	NA
CDC26	ENSG00000176386	0.52326	0.00e+00	0.00e+00	0.507	0.306	Malignant cells	NA
CTNNB1	ENSG00000168036	0.522709	0.00e+00	0.00e+00	0.383	0.211	Malignant cells	NA
SLC12A8	ENSG00000221955	0.521586	0.00e+00	0.00e+00	0.271	0.006	Malignant cells	NA
HNRNPH1	ENSG00000284254	0.519111	0.00e+00	0.00e+00	0.478	0.338	Malignant cells	NA
COA1	ENSG00000106603	0.518107	0.00e+00	0.00e+00	0.594	0.471	Malignant cells	NA
SELENOK	ENSG00000113811	0.515634	0.00e+00	0.00e+00	0.664	0.548	Malignant cells	NA
HPCAL1	ENSG00000115756	0.513328	0.00e+00	0.00e+00	0.428	0.224	Malignant cells	NA
FIS1	ENSG00000214253	0.512932	0.00e+00	0.00e+00	0.751	0.638	Malignant cells	NA
PSMA3	ENSG00000100567	0.512135	0.00e+00	0.00e+00	0.509	0.376	Malignant cells	NA
GLIPR1	ENSG00000139278	0.508599	0.00e+00	0.00e+00	0.311	0.049	Malignant cells	NA
KPNA2	ENSG00000182481	0.508129	0.00e+00	0.00e+00	0.461	0.278	Malignant cells	NA
ATP5PO	ENSG00000241837	0.504275	0.00e+00	0.00e+00	0.855	0.792	Malignant cells	NA
IRS1	ENSG00000169047	0.502875	0.00e+00	0.00e+00	0.28	0.025	Malignant cells	NA
RFC1	ENSG00000035928	0.496933	0.00e+00	0.00e+00	0.528	0.369	Malignant cells	NA
HMGN3	ENSG00000118418	0.495458	0.00e+00	0.00e+00	0.502	0.32	Malignant cells	NA
PGAM1	ENSG00000171314	0.495129	0.00e+00	0.00e+00	0.806	0.699	Malignant cells	NA
OSTC	ENSG00000198856	0.494676	0.00e+00	0.00e+00	0.589	0.48	Malignant cells	NA
EIF3K	ENSG00000282986	0.492712	0.00e+00	0.00e+00	0.993	0.982	Malignant cells	NA
SSBP1	ENSG00000262771	0.48776	0.00e+00	0.00e+00	0.93	0.865	Malignant cells	NA
PARK7	ENSG00000116288	0.486392	0.00e+00	0.00e+00	0.983	0.955	Malignant cells	NA
RPL15	ENSG00000174748	0.482301	0.00e+00	0.00e+00	1	1	Malignant cells	NA
ARL6IP5	ENSG00000144746	0.480931	0.00e+00	0.00e+00	0.464	0.298	Malignant cells	NA
MYEOV	ENSG00000172927	0.480819	0.00e+00	0.00e+00	0.366	0.147	Malignant cells	NA
SAR1A	ENSG00000079332	0.480432	0.00e+00	0.00e+00	0.471	0.295	Malignant cells	NA
CYCS	ENSG00000172115	0.479525	0.00e+00	0.00e+00	0.875	0.785	Malignant cells	NA
NDUFB3	ENSG00000119013	0.47803	0.00e+00	0.00e+00	0.558	0.428	Malignant cells	NA
ADAMTS6	ENSG00000049192	0.474811	0.00e+00	0.00e+00	0.271	0.058	Malignant cells	NA
S100A11	ENSG00000163191	0.473372	0.00e+00	0.00e+00	0.996	0.975	Malignant cells	NA
FAM162A	ENSG00000114023	0.471239	0.00e+00	0.00e+00	0.514	0.38	Malignant cells	NA
PSME2	ENSG00000284889	0.47051	0.00e+00	0.00e+00	0.733	0.667	Malignant cells	NA
CPT1C	ENSG00000169169	0.467175	0.00e+00	0.00e+00	0.293	0.043	Malignant cells	NA
SRRM1	ENSG00000133226	0.466138	0.00e+00	0.00e+00	0.542	0.427	Malignant cells	NA
CCT2	ENSG00000166226	0.465285	0.00e+00	0.00e+00	0.818	0.762	Malignant cells	NA
DPCD	ENSG00000166171	0.464425	0.00e+00	0.00e+00	0.515	0.366	Malignant cells	NA
MARCKS	ENSG00000277443	0.462993	0.00e+00	0.00e+00	0.289	0.058	Malignant cells	NA
GLRX	ENSG00000173221	0.4609	0.00e+00	0.00e+00	0.416	0.218	Malignant cells	NA
TRMT10C	ENSG00000174173	0.459492	0.00e+00	0.00e+00	0.439	0.281	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	2.90e-07	1.50e-06	1733	781	97	23467	Malignant cells	AURKA,BAX,BRCA1,CDCP1,CDK4,COL3A1,CTNNB1,DCTD,DNMT1,GSTP1,HMGA1,HMGB1,ID1,IRS1,PKM,MCL1,MAP1LC3B,NFE2L2,NFKB1,PARP1,RPS6,S100A4,SHC1,ST3GAL4,SOX4,PBK,YWHAZ,AAMDC,SLC25A5,ATG3,BAD,BAG1,BID,HSPA5,BRD4,BTG1,CCNB1,CDK1,CCND1,CD44,DDIT3,DKK1,EGR1,ERCC1,ERRFI1,FIS1,FOXM1,FTL,FUS,GAPDH,HDAC3,HMGB2,HSPA8,HSPB1,IL24,CXCL8,NKIRAS2,LDHA,MTDH,MGMT,SPP1,PABPC1,PGK1,AGPAT2,POMP,PRKDC,PSMB5,PSMG2,PTPN12,RAC1,RAP1B,ERBB3,HNRNPA1,RSF1,S100A11,SDHB,SMC4,SMUG1,SOX10,TPT1,TFAM,TGFA,TMED3,TMEM54,TOP1,WNT5A,YEATS4,MAGEA4,CALR,NPM1,EIF4EBP1,MDK,RCN1,PMVK,EBP,TRIB3,BIRC2
Drug Inactivation by Structure Modification	3.20e-01	8.00e-01	1733	27	3	23467	Malignant cells	GSTP1,GSS,NME1
Aberration of the Drug's Therapeutic Target	6.60e-01	9.60e-01	1733	90	6	23467	Malignant cells	BRCA1,CDK4,NPM1,COMT,AKR1B1,TOP2A
Irregularity in Drug Uptake and Drug Efflux	7.70e-01	9.60e-01	1733	37	2	23467	Malignant cells	SLC3A2,SLC7A5
Epigenetic Alteration of DNA, RNA or Protein	1.00e+00	1.00e+00	1733	455	14	23467	Malignant cells	DNMT1,IRS1,LMNA,TRIP6,PMAIP1,GAPDH,CXCL8,SMC4,TIMP1,CYTOR,MALAT1,GIHCG,GDI2,PPP1R15A

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
	taipale_tf_pairs__ETV5_HOXA2_RSCGGWAATKR_CAP	6.81	0.0742	ETV5; HOXA2 (directAnnotation).	Malignant cells
	taipale_tf_pairs__ETS2_RCCGGAAGTG_HT	6.77	0.0739	ETS2 (directAnnotation).	Malignant cells
	swissregulon__hs__ETV6	6.69	0.0732	ETV6 (directAnnotation).	Malignant cells
	taipale_tf_pairs__ELK1_HOXA1_RCCGGAAGTAATTA_HT	6.6	0.0725	ELK1; HOXA1 (directAnnotation).	Malignant cells
	taipale_tf_pairs__MEIS1_ELF1_NTGCCGGAAGTN_CAP_repr	6.03	0.0681	ELF1; MEIS1 (directAnnotation).	Malignant cells
	jaspar__MA1483.2	5.98	0.0677	ELF2 (directAnnotation).	Malignant cells
	hdpi__TP73	5.98	0.0677	TP73 (directAnnotation).	Malignant cells
	metacluster_191.2	5.71	0.0656	ELK4; NR2C2; NR2C2; NR2C2; NR2C2 (directAnnotation). GABPA (inferredBy_Orthology).	Malignant cells
	swissregulon__hs__ELF2	5.57	0.0645	ELF2 (directAnnotation).	Malignant cells
	metacluster_191.3	5.52	0.0641	EHF; ELF1; ELF1; ELF1; ELF4; ELK1; ELK3; ELK3; ELK4; ELK4; ERF; ETS1; ETS2; ETV3; ETV4; ETV5; FEV; FEV; FLI1; FLI1; GABPA; GABPA; GABPA; GABPA; GABPA; GABPA; SPDEF; ZNF200 (directAnnotation). ELK1; ELK1; ELK3; ELK3; ELK4; ELK4; ETV1; ETV1; ETV4; ETV4; ETV4; ETV5; GABPA; GABPA (inferredBy_Orthology).	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__ETS2_RCCGGAAGTG_HT	8.96	0.0694	ETS2 (directAnnotation).	Malignant cells
	transfac_pro__M04826	7.72	0.0628	EP300 (directAnnotation).	Malignant cells
	metacluster_166.2	6.63	0.057	ELK4; ETS1; ETS1; ETV1; ETV3; ETV4; ETV5; ETV7 (directAnnotation). GABPA (inferredBy_Orthology).	Malignant cells
	taipale_tf_pairs__ETV5_FOXI1_RSCGGATGTTGN_CAP	6.55	0.0566	ETV5; FOXI1 (directAnnotation).	Malignant cells
	metacluster_191.3	6.5	0.0563	EHF; ELF1; ELF1; ELF1; ELF4; ELK1; ELK3; ELK3; ELK4; ELK4; ERF; ETS1; ETS2; ETV3; ETV4; ETV5; FEV; FEV; FLI1; FLI1; GABPA; GABPA; GABPA; GABPA; GABPA; GABPA; SPDEF; ZNF200 (directAnnotation). ELK1; ELK1; ELK3; ELK3; ELK4; ELK4; ETV1; ETV1; ETV4; ETV4; ETV4; ETV5; GABPA; GABPA (inferredBy_Orthology).	Malignant cells
	jaspar__MA1483.2	6.36	0.0556	ELF2 (directAnnotation).	Malignant cells
	metacluster_191.2	6.34	0.0555	ELK4; NR2C2; NR2C2; NR2C2; NR2C2 (directAnnotation). GABPA (inferredBy_Orthology).	Malignant cells
	metacluster_34.4	6.2	0.0547	ETS1; ETS1; ETS1; HCFC1; SIX5; SIX5; SIX5; SIX5; SMARCC2; SMARCC2; THAP11; THAP11; ZNF143; ZNF143; ZNF143; ZNF143 (directAnnotation). TBX2; THAP11; THAP11; ZNF143 (inferredBy_Orthology).	Malignant cells
	hdpi__FLI1	6.15	0.0545	FLI1 (directAnnotation).	Malignant cells
	metacluster_166.4	6.11	0.0543	BCLAF1; EHF; ELF1; ELF1; ELF1; ELF1; ELF1; ELF1; ELF2; ELF2; ELF4; ELK1; ELK1; ELK1; ELK1; ELK1; ELK1; ELK1; ELK1; ELK1; ELK3; ELK3; ELK3; ELK3; ELK4; ERG; ERG; ERG; ERG; ETS1; ETS1; ETS1; ETS1; ETS1; ETV1; ETV1; ETV1; ETV1; ETV2; ETV3; ETV4; ETV4; ETV4; ETV4; ETV4; ETV5; ETV7; FEV; FEV; FLI1; FLI1; FLI1; FLI1; GABPA; GABPA; GABPA; GABPA; GABPA; GABPA; GABPB1; GATAD1; PHF20; ZBTB25; ZBTB40 (directAnnotation). EHF; ELF1; ELF1; ELF3; ELF5; ELK3; ELK4; ERG; ETS1; ETV1; ETV2; ETV4; FLI1; GABPA; GABPA (inferredBy_Orthology).	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
EGR1	metacluster_34.3	up	Malignant cells	NA
ETV4	metacluster_166.2	down	Malignant cells	NA
ETV4	metacluster_191.3	down	Malignant cells	NA
ETV4	metacluster_166.4	down	Malignant cells	NA
GABPB1	metacluster_166.4	down	Malignant cells	NA
ETV4	taipale_tf_pairs__HOXB2_ETV4_ACCGGAAATGAN_CAP	down	Malignant cells	NA
ETV4	taipale_tf_pairs__FOXO1_ETV4_RCCGGAWGTKKN_CAP	down	Malignant cells	NA
ETV4	hdpi__ETV4	down	Malignant cells	NA
ETV4	taipale_tf_pairs__GCM1_ETV4_RTGCGGGCGGAAGTR_CAP	down	Malignant cells	NA
ETV4	metacluster_138.2	down	Malignant cells	NA

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