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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: GSE186960

Dataset summary for GSE186960

Datast information	Dataset	GSE186960
	PMID	35476525
	Raw data ID/link	PRJNA776896
	Organism	Homo sapiens
	Source	Panc1 cell line
	Tissue	Cell line
	Cancer type level1	Pancreatic cancer
	Cancer type level2	Pancreatic ductal adenocarcinoma (PDAC)
	Regimen	gemcitabine
	Drug type	Chemotherapy
	Sample size	resistant 1, sensitive 1
	Cell number	6136
	Extract protocol	DropSeq and 10x genomics
	Data processing	Casava1.7 and CellRanger 6.0.0
	Public date	Public on Mar 21, 2022
	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 GSE186960

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"Gemcitabine"	DB00441	small molecule	RRM1; TYMS; CMPK1	P23921; P04818; P30085

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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
RWDD4	ENSG00000182552	0.289616	1.70e-20	3.78e-16	0.44	0.261	Malignant cells	NA
INPPL1	ENSG00000165458	0.289265	2.32e-32	5.16e-28	0.262	0.056	Malignant cells	NA
UBE4B	ENSG00000130939	0.289155	2.00e-26	4.45e-22	0.353	0.149	Malignant cells	NA
CBX6	ENSG00000183741	0.289133	2.06e-20	4.59e-16	0.6	0.42	Malignant cells	NA
GPATCH2	ENSG00000092978	0.289061	6.08e-23	1.35e-18	0.394	0.201	Malignant cells	NA
HERPUD2	ENSG00000122557	0.289029	1.08e-26	2.41e-22	0.332	0.133	Malignant cells	NA
JOSD1	ENSG00000100221	0.288821	1.97e-24	4.38e-20	0.367	0.17	Malignant cells	NA
GNB2	ENSG00000172354	0.288795	1.36e-19	3.02e-15	0.691	0.544	Malignant cells	NA
PPA1	ENSG00000180817	0.2883	1.86e-21	4.15e-17	0.884	0.815	Malignant cells	NA
BAD	ENSG00000002330	0.288293	1.07e-25	2.39e-21	0.362	0.158	Malignant cells	NA
SNRPD3	ENSG00000100028	0.288108	6.27e-29	1.40e-24	0.982	0.964	Malignant cells	NA
HNRNPUL2	ENSG00000214753	0.288045	7.23e-25	1.61e-20	0.352	0.156	Malignant cells	NA
POFUT1	ENSG00000101346	0.287959	1.79e-25	3.99e-21	0.308	0.119	Malignant cells	NA
CENPB	ENSG00000125817	0.287776	1.02e-25	2.28e-21	0.395	0.185	Malignant cells	NA
RAD23B	ENSG00000119318	0.287758	9.93e-23	2.21e-18	0.715	0.552	Malignant cells	NA
TBC1D20	ENSG00000125875	0.287557	4.29e-26	9.56e-22	0.325	0.128	Malignant cells	NA
ACTN4	ENSG00000282844	0.287253	7.28e-23	1.62e-18	0.969	0.936	Malignant cells	NA
ULK1	ENSG00000177169	0.286782	1.89e-23	4.22e-19	0.334	0.142	Malignant cells	NA
CLSTN1	ENSG00000171603	0.286743	8.24e-25	1.84e-20	0.411	0.203	Malignant cells	NA
CYB561A3	ENSG00000162144	0.286556	2.87e-29	6.39e-25	0.254	0.063	Malignant cells	NA
TMEM222	ENSG00000186501	0.286446	7.19e-28	1.60e-23	0.278	0.086	Malignant cells	NA
RP11-111M22.3	NA	0.286249	9.29e-26	2.07e-21	0.267	0.086	Malignant cells	NA
WIZ	ENSG00000011451	0.286049	1.68e-32	3.74e-28	0.259	0.054	Malignant cells	NA
IFNGR1	ENSG00000027697	0.28586	2.37e-26	5.29e-22	0.293	0.103	Malignant cells	NA
ITPRIPL2	ENSG00000205730	0.285718	1.78e-24	3.96e-20	0.378	0.176	Malignant cells	NA
LRP10	ENSG00000197324	0.285595	2.40e-20	5.34e-16	0.444	0.255	Malignant cells	NA
ZNRF1	ENSG00000186187	0.285461	2.49e-29	5.55e-25	0.283	0.082	Malignant cells	NA
GPT2	ENSG00000166123	0.284751	4.96e-29	1.11e-24	0.266	0.072	Malignant cells	NA
NDUFB7	ENSG00000099795	0.284697	6.12e-26	1.36e-21	0.941	0.901	Malignant cells	NA
PDLIM7	ENSG00000196923	0.284555	2.85e-28	6.36e-24	0.261	0.07	Malignant cells	NA
MTO1	ENSG00000135297	0.28448	1.78e-22	3.97e-18	0.45	0.245	Malignant cells	NA
CFLAR	ENSG00000003402	0.284479	7.49e-28	1.67e-23	0.279	0.085	Malignant cells	NA
DPH5	ENSG00000117543	0.284421	1.43e-28	3.20e-24	0.252	0.064	Malignant cells	NA
HMGCL	ENSG00000117305	0.284235	4.74e-23	1.06e-18	0.339	0.153	Malignant cells	NA
CSNK1E	ENSG00000213923	0.284137	2.07e-21	4.61e-17	0.645	0.46	Malignant cells	NA
TIMP2	ENSG00000035862	0.283692	4.13e-26	9.20e-22	0.274	0.089	Malignant cells	NA
NONO	ENSG00000147140	0.283656	2.21e-21	4.92e-17	0.831	0.738	Malignant cells	NA
ZBTB44	ENSG00000196323	0.283647	1.59e-23	3.54e-19	0.355	0.162	Malignant cells	NA
PTPRA	ENSG00000132670	0.283384	1.13e-20	2.53e-16	0.433	0.245	Malignant cells	NA
RLIM	ENSG00000131263	0.283257	2.27e-24	5.05e-20	0.378	0.179	Malignant cells	NA
MSH6	ENSG00000116062	0.283161	1.12e-14	2.50e-10	0.595	0.466	Malignant cells	NA
XPO5	ENSG00000124571	0.282916	1.05e-23	2.34e-19	0.357	0.165	Malignant cells	NA
SNX24	ENSG00000064652	0.282829	2.20e-24	4.90e-20	0.308	0.123	Malignant cells	NA
HABP4	ENSG00000130956	0.282801	4.57e-30	1.02e-25	0.25	0.056	Malignant cells	NA
RNF130	ENSG00000113269	0.282772	1.01e-19	2.26e-15	0.474	0.291	Malignant cells	NA
ID3	ENSG00000283060	0.28274	7.20e-11	1.60e-06	0.919	0.913	Malignant cells	NA
RNF19A	ENSG00000034677	0.28253	1.02e-23	2.26e-19	0.351	0.159	Malignant cells	NA
GSTT1	ENSG00000277656	0.282447	2.11e-19	4.70e-15	0.457	0.279	Malignant cells	NA
BBX	ENSG00000114439	0.282303	1.19e-18	2.66e-14	0.638	0.473	Malignant cells	NA
MAP9	ENSG00000164114	0.282295	2.47e-24	5.51e-20	0.476	0.256	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	1.10e-17	5.70e-17	2539	781	165	23467	Malignant cells	PPP2R5A,ANXA2,BAX,CDCP1,CDK4,CDK6,CDKN1A,CERS2,CFLAR,TP53,CUL5,DNMT1,FUBP1,HIF1A,HMGB1,HMOX1,HSPA1A,HOXB3,ISG15,PKM,MAPK1,MAP1LC3B,MTOR,NFE2L2,PARP1,PTPN11,RALBP1,RHOA,RPS6,S100A4,SFRP1,SHC1,SOX4,STMN1,TYMS,VEGFA,YWHAZ,NT5C2,ADAM17,SLC25A5,AGR2,AIFM1,AKAP12,AKT1,ANXA1,TFAP2A,ARID1A,BAD,HSPA5,BIRC6,BRD4,BRD7,BTG1,CAV2,CCNB1,CDK1,CCND1,CD44,CDK2,HSPD1,CLTC,COL1A1,CTNND1,DDIT3,DHFR,EIF3A,HSP90B1,EP300,ERRFI1,EZH2,EZR,FAT1,FGFR1,FIS1,FOXM1,FOXO3,FTL,FUS,GAPDH,GRB2,HDAC1,HMGB2,HNRNPU,HSPA8,HSPB1,HOXC9,IDH1,EIF4A1,EIF4A3,NFKBIA,ITGB1,AK4,KIF11,LAMP2,LDHA,LRRFIP1,MXD4,MDM2,MDM4,MGMT,MAPK3,MAP2K2,MSH6,MYBL2,MYO10,NOTCH2,NQO1,NUCKS1,PABPC1,PDCD10,PGK1,PIAS3,AGPAT2,PLK1,PRKDC,PSMG2,PURA,RANGAP1,HRAS,REV3L,RND3,HNRNPA1,ROCK2,RPP21,RSF1,S100A11,SDHB,SMC4,SMARCC1,SOD2,SRSF2,TPT1,TMEM54,TOP1,TRIM27,UBE2C,USP22,ULK1,WEE1,WLS,YES1,ZNF217,ENO1,FASN,PFKL,RASSF8,GNAS,BRCA2,PMS2,NPM1,EIF4EBP1,MDK,RCN1,BRD2,SQLE,TM7SF2,SAFB2,EBP,ACAP2,UBR5,TRIB3,APP,WTAP,ACAT2,CDK7
Aberration of the Drug's Therapeutic Target	1.60e-02	3.90e-02	2539	90	17	23467	Malignant cells	CDK4,CDK6,TP53,MTOR,AKT1,DHFR,EZH2,FGFR1,IDH1,MAP2K2,MSH6,JAK1,SF3B1,NPM1,COMT,AKR1B1,TOP2A
Drug Inactivation by Structure Modification	3.30e-01	4.60e-01	2539	27	4	23467	Malignant cells	NT5C2,SOD2,BCHE,NME1
Irregularity in Drug Uptake and Drug Efflux	3.70e-01	4.60e-01	2539	37	5	23467	Malignant cells	SLC3A2,ABCC1,SLC7A5,SLC7A11,SLC29A1
Epigenetic Alteration of DNA, RNA or Protein	1.00e+00	1.00e+00	2539	455	20	23467	Malignant cells	TP53,DNMT1,H2AFY,EIF4G2,LMNA,TYMS,PMAIP1,EZH2,FOXO3,GAPDH,IDH1,MAPK3,SMC4,TIMP1,SNHG14,MALAT1,GDI2,PPP1R15A,MT-CO2,GABPB1-AS1

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_174.3	5.72	0.0646	MBD2; NFYA; NFYB; NFYC; PBX3 (directAnnotation).	Malignant cells
	metacluster_174.2	5.58	0.0638	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
	metacluster_174.6	4.53	0.0572	NFYA; NFYB; NFYB; NFYC (directAnnotation).	Malignant cells
	jaspar__MA0502.2	4.05	0.0543	NFYB (directAnnotation).	Malignant cells
	metacluster_144.8	3.74	0.0524	ZNF30; ZNF30 (directAnnotation).	Malignant cells
	jaspar__MA1933.1	3.71	0.0522	SREBF2 (directAnnotation).	Malignant cells
	dbtfbs__GMEB1_K562_ENCSR928KOR_merged_N1	3.53	0.0511	GMEB1 (directAnnotation).	Malignant cells
	metacluster_156.2	3.47	0.0507	ATF3; ATF4; ATF4; ATF4; ATF4; ATF4; ATF4; CEBPG; CEBPG; DDIT3; MYC (directAnnotation). ATF4; ATF4; ATF4; CEBPG; DDIT3 (inferredBy_Orthology).	Malignant cells
	transfac_pro__M04918	3.34	0.0499	EGR1 (directAnnotation).	Malignant cells
	metacluster_7.5	3.33	0.0498	PLAGL1; PLAGL1 (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_191.2	5.8	0.0654	ELK4; NR2C2; NR2C2; NR2C2; NR2C2 (directAnnotation). GABPA (inferredBy_Orthology).	Malignant cells
	metacluster_191.3	5.51	0.0634	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
	taipale_tf_pairs__ETS2_RCCGGAAGTG_HT	5.51	0.0634	ETS2 (directAnnotation).	Malignant cells
	metacluster_166.4	5.08	0.0604	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__ETV5_HOXA2_RSCGGWAATKR_CAP	4.83	0.0585	ETV5; HOXA2 (directAnnotation).	Malignant cells
	taipale_tf_pairs__FOXO1_ELK3_RCCGGAWGTKKW_CAP	4.72	0.0578	ELK3; FOXO1 (directAnnotation).	Malignant cells
	hdpi__TP73	4.66	0.0573	TP73 (directAnnotation).	Malignant cells
	jaspar__MA1483.2	4.63	0.0571	ELF2 (directAnnotation).	Malignant cells
	swissregulon__hs__ETV6	4.52	0.0563	ETV6 (directAnnotation).	Malignant cells
	metacluster_166.2	4.48	0.0561	ELK4; ETS1; ETS1; ETV1; ETV3; ETV4; ETV5; ETV7 (directAnnotation). 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
ERF	metacluster_191.3	up	Malignant cells	NA
ETV5	metacluster_191.3	up	Malignant cells	NA
ETV5	metacluster_166.4	up	Malignant cells	NA
GATAD1	metacluster_166.4	up	Malignant cells	NA
ETV5	taipale_tf_pairs__ETV5_HOXA2_RSCGGWAATKR_CAP	up	Malignant cells	NA
ETV5	metacluster_166.2	up	Malignant cells	NA
ERF	metacluster_138.2	up	Malignant cells	NA
ETV5	metacluster_138.2	up	Malignant cells	NA
ZNF580	metacluster_138.2	up	Malignant cells	NA
EP300	transfac_pro__M04826	up	Malignant cells	NA

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