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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
CMSS1	ENSG00000184220	-0.368146	1.75e-26	3.90e-22	0.702	0.824	Malignant cells	NA
NPTN	ENSG00000156642	-0.368197	8.05e-28	1.79e-23	0.283	0.457	Malignant cells	NA
CPSF2	ENSG00000165934	-0.368526	2.09e-20	4.65e-16	0.48	0.595	Malignant cells	NA
ZBTB8OS	ENSG00000176261	-0.369124	2.77e-33	6.17e-29	0.706	0.842	Malignant cells	NA
SRPR	NA	-0.369792	2.24e-23	5.00e-19	0.463	0.6	Malignant cells	NA
ISCU	ENSG00000136003	-0.369862	5.61e-27	1.25e-22	0.603	0.739	Malignant cells	NA
CYB5B	ENSG00000103018	-0.370128	1.22e-27	2.73e-23	0.863	0.944	Malignant cells	NA
ZC3H13	ENSG00000123200	-0.370324	2.50e-25	5.57e-21	0.684	0.782	Malignant cells	NA
CXXC5	ENSG00000171604	-0.370738	7.99e-28	1.78e-23	0.217	0.383	Malignant cells	NA
RAB11A	ENSG00000103769	-0.371163	3.58e-24	7.97e-20	0.569	0.693	Malignant cells	NA
F2R	ENSG00000181104	-0.371626	1.44e-42	3.21e-38	0.155	0.352	Malignant cells	NA
NDUFV3	ENSG00000160194	-0.371721	8.77e-20	1.95e-15	0.497	0.607	Malignant cells	NA
RSRC1	ENSG00000174891	-0.37203	2.68e-21	5.97e-17	0.452	0.572	Malignant cells	NA
LTV1	ENSG00000135521	-0.372527	9.52e-22	2.12e-17	0.636	0.728	Malignant cells	NA
RP3-417G15.1	NA	-0.372946	0.00e+00	0.00e+00	0.029	0.281	Malignant cells	NA
RPS8P3	ENSG00000215457	-0.373096	0.00e+00	0.00e+00	0	0.251	Malignant cells	NA
RP11-571F15.3	NA	-0.373372	0.00e+00	0.00e+00	0.003	0.258	Malignant cells	NA
VIMP	NA	-0.373494	2.02e-28	4.50e-24	0.606	0.745	Malignant cells	NA
FAM96A	NA	-0.375136	2.45e-26	5.45e-22	0.323	0.483	Malignant cells	NA
TAPBP	ENSG00000206281	-0.375488	0.00e+00	0.00e+00	0.001	0.256	Malignant cells	NA
NDUFA11	ENSG00000174886	-0.375561	2.65e-36	5.89e-32	0.821	0.928	Malignant cells	NA
HDAC8	ENSG00000147099	-0.376284	0.00e+00	0.00e+00	0	0.251	Malignant cells	NA
DDX18	ENSG00000088205	-0.376707	5.37e-30	1.20e-25	0.758	0.871	Malignant cells	NA
RPS18P12	ENSG00000230897	-0.378666	0.00e+00	0.00e+00	0.003	0.264	Malignant cells	NA
YBX1P10	ENSG00000213866	-0.378869	0.00e+00	0.00e+00	0.032	0.288	Malignant cells	NA
MRPL33	ENSG00000243147	-0.378926	1.23e-31	2.74e-27	0.833	0.941	Malignant cells	NA
CTSC	ENSG00000109861	-0.378955	9.99e-24	2.23e-19	0.352	0.509	Malignant cells	NA
EEF1A1P5	ENSG00000196205	-0.379111	0.00e+00	0.00e+00	0.038	0.301	Malignant cells	NA
EIF4G2	ENSG00000110321	-0.379589	9.77e-42	2.18e-37	0.997	1	Malignant cells	NA
MCM3	ENSG00000112118	-0.379683	8.06e-27	1.80e-22	0.74	0.858	Malignant cells	NA
EXOSC3	ENSG00000107371	-0.379801	1.48e-25	3.29e-21	0.369	0.524	Malignant cells	NA
MPHOSPH6	ENSG00000135698	-0.380117	1.62e-26	3.61e-22	0.341	0.501	Malignant cells	NA
C12orf75	ENSG00000235162	-0.380177	1.84e-19	4.11e-15	0.397	0.519	Malignant cells	NA
MRPL13	ENSG00000172172	-0.380229	6.19e-33	1.38e-28	0.765	0.891	Malignant cells	NA
NOSIP	ENSG00000142546	-0.380524	2.76e-25	6.14e-21	0.371	0.516	Malignant cells	NA
CNBP	ENSG00000169714	-0.380563	3.92e-44	8.77e-40	0.976	0.997	Malignant cells	NA
RGS19	ENSG00000171700	-0.380993	2.20e-41	4.91e-37	0.176	0.375	Malignant cells	NA
CD44	ENSG00000026508	-0.381021	1.24e-26	2.77e-22	0.818	0.907	Malignant cells	NA
UQCRQ	ENSG00000164405	-0.381128	0.00e+00	0.00e+00	0.991	1	Malignant cells	NA
CDCA7L	ENSG00000164649	-0.381534	8.91e-20	1.98e-15	0.429	0.543	Malignant cells	NA
SAFB2	ENSG00000130254	-0.383214	1.14e-21	2.53e-17	0.401	0.534	Malignant cells	NA
PINX1	ENSG00000254093	-0.383377	0.00e+00	8.41e-45	0.15	0.362	Malignant cells	NA
CENPN	ENSG00000166451	-0.383569	6.63e-23	1.48e-18	0.416	0.552	Malignant cells	NA
GEMIN6	ENSG00000152147	-0.383738	8.00e-29	1.78e-24	0.337	0.513	Malignant cells	NA
USP8	ENSG00000138592	-0.384008	1.06e-21	2.36e-17	0.445	0.569	Malignant cells	NA
HSD17B11	ENSG00000198189	-0.385684	2.17e-37	4.83e-33	0.193	0.383	Malignant cells	NA
HNRNPH2	ENSG00000126945	-0.385807	0.00e+00	0.00e+00	0	0.258	Malignant cells	NA
NSRP1P1	ENSG00000235613	-0.386153	0.00e+00	0.00e+00	0.019	0.269	Malignant cells	NA
AKAP8	ENSG00000105127	-0.386423	1.22e-34	2.71e-30	0.22	0.408	Malignant cells	NA
DDX17	ENSG00000100201	-0.386564	4.37e-34	9.73e-30	0.764	0.891	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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