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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
AGAP2-AS1	ENSG00000255737	0.277745	0.00e+00	1.05e-43	0.728	0.581	Malignant cells	NA
MRPL48	ENSG00000175581	0.277262	0.00e+00	0.00e+00	0.996	0.988	Malignant cells	NA
CCNH	ENSG00000134480	0.277233	8.57e-38	1.55e-33	0.824	0.738	Malignant cells	NA
POLR2K	ENSG00000147669	0.277136	0.00e+00	0.00e+00	1	0.998	Malignant cells	NA
TBC1D7	ENSG00000145979	0.276696	3.90e-33	7.06e-29	0.945	0.927	Malignant cells	NA
NENF	ENSG00000117691	0.276173	0.00e+00	0.00e+00	1	1	Malignant cells	NA
ERP29	ENSG00000089248	0.276126	0.00e+00	0.00e+00	0.998	0.998	Malignant cells	NA
UFC1	ENSG00000143222	0.27579	0.00e+00	0.00e+00	0.975	0.954	Malignant cells	NA
AHCY	ENSG00000101444	0.274791	0.00e+00	0.00e+00	0.998	0.997	Malignant cells	NA
GABRB3	ENSG00000166206	0.274293	0.00e+00	2.45e-42	0.629	0.47	Malignant cells	NA
EIF3K	ENSG00000282986	0.273248	0.00e+00	0.00e+00	1	1	Malignant cells	NA
RP11-486G15.2	NA	0.273187	0.00e+00	0.00e+00	0.364	0.182	Malignant cells	NA
ROPN1B	ENSG00000114547	0.272044	0.00e+00	1.40e-45	0.381	0.222	Malignant cells	NA
PARL	ENSG00000175193	0.272006	0.00e+00	0.00e+00	0.998	0.996	Malignant cells	NA
MOCS2	ENSG00000164172	0.271732	0.00e+00	2.24e-44	0.968	0.943	Malignant cells	NA
DUSP12	ENSG00000081721	0.271726	3.79e-42	6.86e-38	0.782	0.674	Malignant cells	NA
MESDC2	NA	0.27152	0.00e+00	0.00e+00	0.973	0.946	Malignant cells	NA
TGFB1	ENSG00000105329	0.271496	0.00e+00	5.64e-42	0.376	0.218	Malignant cells	NA
MDH1	ENSG00000014641	0.27087	0.00e+00	0.00e+00	0.985	0.974	Malignant cells	NA
COPS5	ENSG00000121022	0.270402	0.00e+00	2.80e-45	0.962	0.929	Malignant cells	NA
LINC00511	ENSG00000227036	0.270258	0.00e+00	6.28e-43	0.97	0.932	Malignant cells	NA
UBE2L3	ENSG00000185651	0.2702	0.00e+00	0.00e+00	1	1	Malignant cells	NA
HSD17B1	ENSG00000108786	0.269959	4.24e-41	7.67e-37	0.559	0.407	Malignant cells	NA
MTAP	ENSG00000099810	0.269853	0.00e+00	1.85e-43	0.569	0.404	Malignant cells	NA
MRPL10	ENSG00000159111	0.269806	0.00e+00	1.54e-44	0.914	0.855	Malignant cells	NA
RP11-1102P16.1	NA	0.269525	0.00e+00	0.00e+00	0.347	0.182	Malignant cells	NA
HRK	ENSG00000135116	0.269412	0.00e+00	0.00e+00	0.352	0.18	Malignant cells	NA
RPS24	ENSG00000138326	0.269302	0.00e+00	0.00e+00	1	1	Malignant cells	NA
FARP1	ENSG00000152767	0.26915	6.42e-41	1.16e-36	0.933	0.883	Malignant cells	NA
AC007405.6	NA	0.269109	0.00e+00	0.00e+00	0.285	0.1	Malignant cells	NA
BRI3	ENSG00000164713	0.268265	0.00e+00	0.00e+00	1	1	Malignant cells	NA
MPHOSPH10	ENSG00000124383	0.268233	3.40e-41	6.16e-37	0.899	0.834	Malignant cells	NA
TMEM199	ENSG00000244045	0.268179	2.21e-42	4.00e-38	0.7	0.563	Malignant cells	NA
IDH3G	ENSG00000067829	0.267941	0.00e+00	0.00e+00	0.977	0.956	Malignant cells	NA
LRTOMT	ENSG00000284922	0.267876	2.10e-44	3.89e-40	0.532	0.374	Malignant cells	NA
AKAP11	ENSG00000023516	0.267852	0.00e+00	0.00e+00	0.456	0.28	Malignant cells	NA
LINC00518	ENSG00000183674	0.267447	5.29e-29	9.58e-25	0.684	0.568	Malignant cells	NA
PSAT1	ENSG00000135069	0.267432	4.05e-42	7.33e-38	0.753	0.626	Malignant cells	NA
COX5A	ENSG00000178741	0.266881	0.00e+00	0.00e+00	1	1	Malignant cells	NA
GGH	ENSG00000137563	0.26612	0.00e+00	0.00e+00	0.975	0.944	Malignant cells	NA
AIMP2	ENSG00000106305	0.266055	2.21e-42	4.00e-38	0.696	0.561	Malignant cells	NA
TSR2	ENSG00000158526	0.266005	1.38e-36	2.50e-32	0.808	0.73	Malignant cells	NA
NR2F2	ENSG00000185551	0.26592	4.06e-38	7.34e-34	0.659	0.516	Malignant cells	NA
KIAA0947	NA	0.265817	1.48e-29	2.68e-25	0.744	0.661	Malignant cells	NA
CXorf38	ENSG00000185753	0.265795	0.00e+00	0.00e+00	0.376	0.21	Malignant cells	NA
EPB41L4A-AS1	ENSG00000224032	0.265709	4.76e-44	8.51e-40	0.968	0.949	Malignant cells	NA
MRPL22	ENSG00000082515	0.265549	0.00e+00	0.00e+00	0.98	0.978	Malignant cells	NA
WDR41	ENSG00000164253	0.264801	0.00e+00	8.09e-42	0.561	0.397	Malignant cells	NA
GTF2F2	ENSG00000188342	0.264383	3.32e-39	6.02e-35	0.832	0.731	Malignant cells	NA
NHSL1	ENSG00000135540	0.263489	4.32e-25	7.82e-21	0.68	0.573	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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