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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: GSE108397

Dataset summary for GSE108397

Datast information	Dataset	GSE108397
	PMID	30061114
	Raw data ID/link	PRJNA427121
	Organism	Homo sapiens
	Source	451Lu cell line
	Tissue	Cell line
	Cancer type level1	Melanoma
	Cancer type level2	Melanoma
	Regimen	PLX-4720
	Drug type	Targeted therapy
	Sample size	resistant 1, sensitive 1
	Cell number	6548
	Extract protocol	10x genomics
	Data processing	CellRanger 1.3.1
	Public date	Public on Jul 01, 2018
	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 GSE108397

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"PLX-4720"	DB06999	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
PRC1	ENSG00000198901	-0.268714	2.73e-23	4.93e-19	0.651	0.719	Malignant cells	NA
TRIP12	ENSG00000153827	-0.268773	1.62e-36	2.93e-32	0.631	0.729	Malignant cells	NA
MFSD1	ENSG00000118855	-0.268855	3.80e-36	6.88e-32	0.338	0.467	Malignant cells	NA
FIGNL1	ENSG00000132436	-0.269252	9.91e-38	1.79e-33	0.36	0.499	Malignant cells	NA
NOL10	ENSG00000115761	-0.269419	2.82e-37	5.11e-33	0.615	0.725	Malignant cells	NA
UBA6	ENSG00000033178	-0.269513	1.38e-41	2.50e-37	0.281	0.428	Malignant cells	NA
SLC35F2	ENSG00000110660	-0.269532	5.73e-34	1.04e-29	0.43	0.561	Malignant cells	NA
FIP1L1	ENSG00000145216	-0.269817	9.43e-36	1.71e-31	0.453	0.574	Malignant cells	NA
UBE2O	ENSG00000175931	-0.26986	3.09e-34	5.58e-30	0.469	0.579	Malignant cells	NA
DNAJA1	ENSG00000086061	-0.270352	3.41e-37	6.17e-33	0.924	0.963	Malignant cells	NA
PPIP5K2	ENSG00000145725	-0.270398	1.86e-34	3.37e-30	0.54	0.649	Malignant cells	NA
PCGF6	ENSG00000156374	-0.270426	1.89e-37	3.42e-33	0.46	0.582	Malignant cells	NA
ARCN1	ENSG00000095139	-0.27052	6.22e-35	1.13e-30	0.486	0.604	Malignant cells	NA
SAPCD2	ENSG00000186193	-0.27096	1.11e-39	2.02e-35	0.289	0.429	Malignant cells	NA
ITSN1	ENSG00000205726	-0.271084	0.00e+00	5.23e-42	0.315	0.475	Malignant cells	NA
GMPR	ENSG00000137198	-0.271234	4.93e-40	8.92e-36	0.515	0.651	Malignant cells	NA
PKM	ENSG00000067225	-0.27147	0.00e+00	0.00e+00	1	1	Malignant cells	NA
RALA	ENSG00000006451	-0.271484	0.00e+00	0.00e+00	0.922	0.96	Malignant cells	NA
SRGAP1	ENSG00000196935	-0.271555	1.06e-33	1.92e-29	0.449	0.569	Malignant cells	NA
MOGS	ENSG00000115275	-0.27157	0.00e+00	0.00e+00	0.241	0.407	Malignant cells	NA
LRRC45	ENSG00000169683	-0.271622	1.22e-35	2.20e-31	0.449	0.574	Malignant cells	NA
CSNK2B	ENSG00000230700	-0.271959	0.00e+00	0.00e+00	0.963	0.988	Malignant cells	NA
HEY1	ENSG00000164683	-0.271964	1.91e-34	3.45e-30	0.514	0.633	Malignant cells	NA
POLR2J	ENSG00000005075	-0.272149	0.00e+00	0.00e+00	1	1	Malignant cells	NA
HNRNPU	ENSG00000153187	-0.272199	0.00e+00	9.11e-44	0.904	0.96	Malignant cells	NA
DPM3	ENSG00000179085	-0.272294	1.02e-43	1.84e-39	0.631	0.742	Malignant cells	NA
BAZ1A	ENSG00000198604	-0.2723	1.71e-35	3.10e-31	0.568	0.672	Malignant cells	NA
PTPRG	ENSG00000144724	-0.272335	1.41e-35	2.55e-31	0.507	0.625	Malignant cells	NA
IPO9	ENSG00000198700	-0.272374	5.29e-40	9.57e-36	0.371	0.512	Malignant cells	NA
LCOR	ENSG00000196233	-0.272627	0.00e+00	0.00e+00	0.235	0.41	Malignant cells	NA
KCTD13	ENSG00000174943	-0.272775	0.00e+00	0.00e+00	0.219	0.385	Malignant cells	NA
B4GALT3	ENSG00000158850	-0.272808	8.37e-43	1.51e-38	0.675	0.769	Malignant cells	NA
DHX37	ENSG00000150990	-0.272957	1.40e-45	2.46e-41	0.323	0.476	Malignant cells	NA
GORASP2	ENSG00000115806	-0.273084	0.00e+00	8.41e-45	0.765	0.86	Malignant cells	NA
CALM1	ENSG00000198668	-0.27343	0.00e+00	0.00e+00	1	1	Malignant cells	NA
BOLA3	ENSG00000163170	-0.27359	0.00e+00	0.00e+00	0.999	0.999	Malignant cells	NA
UBA2	ENSG00000126261	-0.273619	0.00e+00	0.00e+00	0.922	0.966	Malignant cells	NA
CMTM3	ENSG00000140931	-0.274024	9.21e-38	1.67e-33	0.594	0.701	Malignant cells	NA
TRIB1	ENSG00000173334	-0.274244	0.00e+00	0.00e+00	0.206	0.368	Malignant cells	NA
LINC00152	NA	-0.274668	0.00e+00	0.00e+00	0.998	1	Malignant cells	NA
RING1	ENSG00000228520	-0.274687	2.36e-40	4.27e-36	0.413	0.551	Malignant cells	NA
RIOK1	ENSG00000124784	-0.27482	8.73e-32	1.58e-27	0.527	0.625	Malignant cells	NA
MBD6	ENSG00000166987	-0.274918	0.00e+00	0.00e+00	0.216	0.384	Malignant cells	NA
ACADM	ENSG00000117054	-0.275244	1.42e-43	2.55e-39	0.794	0.865	Malignant cells	NA
ZNFX1	ENSG00000124201	-0.275263	1.26e-44	2.31e-40	0.283	0.436	Malignant cells	NA
RIT1	ENSG00000143622	-0.275325	4.85e-43	8.77e-39	0.208	0.35	Malignant cells	NA
SAFB2	ENSG00000130254	-0.275333	2.30e-35	4.15e-31	0.528	0.64	Malignant cells	NA
RNF182	ENSG00000180537	-0.275393	0.00e+00	0.00e+00	0.142	0.331	Malignant cells	NA
USP34	ENSG00000115464	-0.275459	0.00e+00	6.26e-43	0.802	0.871	Malignant cells	NA
EFCAB7	ENSG00000203965	-0.275524	2.24e-44	4.18e-40	0.213	0.365	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	3.00e-18	1.50e-17	2772	781	177	23467	Malignant cells	PPP2R5A,ADAM10,AKAP1,AKT2,ANXA2,AURKA,BECN1,BRCA1,CDK4,CERS2,CTNNB1,DNMT1,DUSP6,EPAS1,GLS,GSK3B,GSTP1,SLC2A1,HEY1,HIF1A,HMGA2,HMGB1,EIF4G1,ISG15,JUN,PKM,RPS6KA5,MAGEA12,MCL1,MEF2D,MAPK1,MAP1LC3B,MTOR,NFE2L2,NFKB1,PARP1,PEA15,PPARG,RALBP1,RPS6,SFRP1,SHC1,ST3GAL4,SOX4,SPRY2,TGFB1,TIMP3,PBK,TYMS,XIAP,YWHAZ,AIFM1,AKAP12,TFAP2A,ATG3,ATM,BAG1,HSPA5,BRD4,BTG1,CCNA2,CCND1,CDC27,CDK2,CDKN2A,CDS2,HSPD1,CLTC,CAPNS1,CUL4A,DCK,DDB1,E2F6,EIF3A,ERCC1,ERRFI1,EZH2,EZR,FGFR1,FN1,FOXM1,FTL,FUS,GAPDH,G6PD,GRB2,GCLM,GSR,SLC16A3,HAX1,HDAC1,HDAC3,HMGB2,HNRNPU,HSPA8,HK1,HK2,EIF4A1,EIF5A2,ITGB1,KEAP1,LAMP2,LATS2,LDHA,LRRFIP1,MTDH,MXD4,MAGEA3,NF2,MGMT,MITF,MOB1A,NDST1,IKBKG,NOTCH2,NQO1,PGK1,PIK3CD,AGPAT2,POMP,PSMB5,PSMG2,PTPN1,PTPN12,PTPN18,RAP1A,RAP1B,NRAS,RRM2,ROCK2,RUNX3,S100A11,SFPQ,SMC4,SMARCC1,SNAI2,SOCS3,SRSF2,RBPJ,SUZ12,TPT1,TNFSF13B,TOP1,TWF1,VDR,WLS,YBX1,ENO1,FASN,IDH3A,PFKL,PFKFB3,SLC16A1,CALR,SMARCA4,NPM1,DUSP9,GFPT1,IL6R,FOXK2,LSS,MDK,TRIM37,PPP3CA,RCN1,BRD2,SOAT1,SQLE,SPHK1,SGPL1,SAFB2,G3BP1,PMVK,
Irregularity in Drug Uptake and Drug Efflux	1.40e-01	3.50e-01	2772	37	7	23467	Malignant cells	SLC3A2,ABCB5,SLC2A1,ABCF2,SLC7A5,SLC7A11,SLC29A1
Aberration of the Drug's Therapeutic Target	6.30e-01	7.90e-01	2772	90	10	23467	Malignant cells	AKT2,BRCA1,CDK4,MTOR,CDKN2A,EZH2,FGFR1,JAK1,NPM1,TOP2A
Drug Inactivation by Structure Modification	6.30e-01	7.90e-01	2772	27	3	23467	Malignant cells	GSTP1,DCK,CMPK1
Epigenetic Alteration of DNA, RNA or Protein	1.00e+00	1.00e+00	2772	455	22	23467	Malignant cells	BECN1,DNMT1,GSK3B,H2AFY,EIF4G2,LMNA,PPARG,SPRY2,TRIP6,TYMS,XIAP,PMAIP1,CDKN2A,EZH2,GAPDH,SMC4,TIMP1,TNFSF13B,MALAT1,PPP1R15A,MT-CO2,DLEU1

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
	jaspar__MA1933.1	5.55	0.0574	SREBF2 (directAnnotation).	Malignant cells
	metacluster_191.2	5.33	0.0561	ELK4; NR2C2; NR2C2; NR2C2; NR2C2 (directAnnotation). GABPA (inferredBy_Orthology).	Malignant cells
	taipale_tf_pairs__ETS2_RCCGGAAGTG_HT	5.12	0.0549	ETS2 (directAnnotation).	Malignant cells
	metacluster_166.4	5.04	0.0544	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
	taipale_tf_pairs__MEIS1_ELF1_NTGCCGGAAGTN_CAP_repr	4.96	0.0539	ELF1; MEIS1 (directAnnotation).	Malignant cells
	metacluster_191.3	4.55	0.0515	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
	swissregulon__hs__ELF2	4.52	0.0513	ELF2 (directAnnotation).	Malignant cells
	taipale_tf_pairs__ELK1_TBX21_TNRCACCGGAAGNN_CAP_repr	4.43	0.0508	ELK1; TBX21 (directAnnotation).	Malignant cells
	taipale_tf_pairs__ETV5_HOXA2_RSCGGWAATKR_CAP	4.38	0.0505	ETV5; HOXA2 (directAnnotation).	Malignant cells
	hdpi__ETV4	4.2	0.0494	ETV4 (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
	metacluster_7.13	3.69	0.0499	ZFX (directAnnotation).	Malignant cells
	metacluster_174.3	3.59	0.0494	MBD2; NFYA; NFYB; NFYC; PBX3 (directAnnotation).	Malignant cells
	metacluster_174.2	3.55	0.0491	CEBPZ; CEBPZ; DRAP1; FOS; FOXI1; FOXI1; HMGXB3; IRF3; NFYA; NFYA; NFYA; NFYA; NFYA; NFYA; NFYA; NFYA; NFYA; NFYB; NFYB; NFYB; NFYB; NFYB; NFYC; NFYC; NFYC; NFYC; NFYC; NFYC; NFYC; PBX3; PBX3; SP2 (directAnnotation). NFYA; NFYA; NFYC; PBX1; PBX3 (inferredBy_Orthology).	Malignant cells
	cisbp__M01863	3.49	0.0488	ZNF711 (inferredBy_Orthology).	Malignant cells
	taipale_tf_pairs__ETS2_RCCGGAAGTG_HT	3.47	0.0487	ETS2 (directAnnotation).	Malignant cells
	transfac_pro__M05578	3.42	0.0484	ZFP92 (inferredBy_Orthology).	Malignant cells
	taipale_cyt_meth__ZNF385D_NCGTCGCGACGN_eDBD_meth	3.41	0.0484	ZNF385D (directAnnotation).	Malignant cells
	jaspar__MA1483.2	3.38	0.0482	ELF2 (directAnnotation).	Malignant cells
	metacluster_151.2	3.33	0.0479	ZNF23 (directAnnotation).	Malignant cells
	metacluster_170.2	3.33	0.0479	KLF1; KLF10; KLF10; KLF11; KLF11; KLF11; KLF12; KLF12; KLF14; KLF15; KLF17; KLF2; KLF5; KLF7; KLF7; KLF8; MAZ; MAZ; PATZ1; SP1; SP1; SP1; SP2; SP2; SP2; SP2; SP2; SP2; SP2; SP2; SP4; SP4; SP5; SP6; SP7; SP8; SP9; ZNF281 (directAnnotation). E2F1; E2F4; KLF10; KLF13; KLF14; KLF17; KLF2; KLF7; SP1; SP1; SP3; SP4; SP5; SP6; SP7 (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
ZFX	metacluster_7.13	up	Malignant cells	NA
ZNF385D	taipale_cyt_meth__ZNF385D_NCGTCGCGACGN_eDBD_meth	up	Malignant cells	NA
MAZ	metacluster_170.2	up	Malignant cells	NA
ZNF580	transfac_pro__M05479	up	Malignant cells	NA
ZFX	metacluster_182.10	up	Malignant cells	NA
ZNF580	metacluster_138.2	up	Malignant cells	NA
NFYC	metacluster_174.3	down	Malignant cells	NA
DRAP1	metacluster_174.2	down	Malignant cells	NA
HMGXB3	metacluster_174.2	down	Malignant cells	NA
NFYC	metacluster_174.2	down	Malignant cells	NA

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