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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
PTPLAD1	NA	-0.421134	9.62e-36	2.14e-31	0.697	0.821	Malignant cells	NA
RNF115	ENSG00000265491	-0.421295	0.00e+00	0.00e+00	0.105	0.348	Malignant cells	NA
ANAPC5	ENSG00000089053	-0.421414	1.43e-33	3.19e-29	0.386	0.569	Malignant cells	NA
FGFR1OP2	ENSG00000111790	-0.42165	7.47e-33	1.66e-28	0.591	0.735	Malignant cells	NA
SCNM1	ENSG00000163156	-0.421705	0.00e+00	1.56e-43	0.185	0.404	Malignant cells	NA
LAMB1	ENSG00000091136	-0.422146	0.00e+00	0.00e+00	0.049	0.271	Malignant cells	NA
SVIP	ENSG00000198168	-0.422386	2.05e-22	4.57e-18	0.346	0.483	Malignant cells	NA
RP11-864N7.2	NA	-0.422428	1.75e-29	3.90e-25	0.36	0.524	Malignant cells	NA
SRP72	ENSG00000174780	-0.422753	2.26e-34	5.04e-30	0.594	0.742	Malignant cells	NA
AC018463.5	NA	-0.423281	0.00e+00	0.00e+00	0	0.287	Malignant cells	NA
ZFAS1	ENSG00000177410	-0.423984	7.61e-33	1.69e-28	0.853	0.946	Malignant cells	NA
CAMSAP2	ENSG00000118200	-0.42412	1.51e-36	3.36e-32	0.256	0.453	Malignant cells	NA
LYAR	ENSG00000145220	-0.424689	3.75e-25	8.36e-21	0.823	0.898	Malignant cells	NA
HCFC1	ENSG00000172534	-0.424822	0.00e+00	0.00e+00	0	0.282	Malignant cells	NA
TMEM43	ENSG00000170876	-0.424971	1.21e-38	2.70e-34	0.27	0.474	Malignant cells	NA
CTGF	NA	-0.425092	8.09e-11	1.80e-06	0.255	0.344	Malignant cells	NA
PAK2	ENSG00000180370	-0.425532	1.82e-42	4.05e-38	0.861	0.954	Malignant cells	NA
KDSR	ENSG00000119537	-0.426139	3.43e-39	7.64e-35	0.23	0.433	Malignant cells	NA
PCNA	ENSG00000132646	-0.426149	7.57e-30	1.69e-25	0.782	0.895	Malignant cells	NA
HSPB1	ENSG00000106211	-0.426983	2.22e-28	4.95e-24	0.549	0.673	Malignant cells	NA
PFN2	ENSG00000070087	-0.427339	4.41e-39	9.81e-35	0.853	0.946	Malignant cells	NA
RP11-889L3.1	NA	-0.427799	0.00e+00	0.00e+00	0.022	0.305	Malignant cells	NA
SMIM4	ENSG00000168273	-0.428277	1.42e-29	3.15e-25	0.33	0.499	Malignant cells	NA
JUP	ENSG00000173801	-0.42847	0.00e+00	0.00e+00	0.004	0.277	Malignant cells	NA
HSP90B2P	ENSG00000259706	-0.429301	0.00e+00	0.00e+00	0.022	0.297	Malignant cells	NA
NDUFS4	ENSG00000164258	-0.42952	2.02e-32	4.49e-28	0.411	0.585	Malignant cells	NA
LIX1L	ENSG00000271601	-0.430172	0.00e+00	0.00e+00	0.001	0.278	Malignant cells	NA
MCM6	ENSG00000076003	-0.431321	4.99e-24	1.11e-19	0.364	0.506	Malignant cells	NA
FKBP10	ENSG00000141756	-0.431704	0.00e+00	0.00e+00	0.001	0.288	Malignant cells	NA
H2AFY	NA	-0.432256	2.68e-41	5.97e-37	0.8	0.923	Malignant cells	NA
HAUS1	ENSG00000152240	-0.432675	6.48e-31	1.44e-26	0.334	0.501	Malignant cells	NA
RBFA	ENSG00000101546	-0.432769	1.38e-33	3.08e-29	0.328	0.511	Malignant cells	NA
RP3-432I18.1	NA	-0.434031	0.00e+00	0.00e+00	0	0.285	Malignant cells	NA
CTTN	ENSG00000288401	-0.434071	6.31e-44	1.40e-39	0.777	0.907	Malignant cells	NA
MRPS5	ENSG00000144029	-0.434502	1.50e-36	3.34e-32	0.686	0.808	Malignant cells	NA
PPIP5K2	ENSG00000145725	-0.434807	0.00e+00	0.00e+00	0.013	0.277	Malignant cells	NA
FUBP1	ENSG00000162613	-0.436026	3.68e-38	8.20e-34	0.705	0.838	Malignant cells	NA
IMP3	ENSG00000177971	-0.436566	0.00e+00	7.71e-44	0.232	0.464	Malignant cells	NA
VAPA	ENSG00000101558	-0.436915	4.66e-39	1.04e-34	0.813	0.92	Malignant cells	NA
YBX1P2	ENSG00000231167	-0.436936	0.00e+00	0.00e+00	0.036	0.328	Malignant cells	NA
RNF113A	ENSG00000125352	-0.436984	0.00e+00	0.00e+00	0.117	0.352	Malignant cells	NA
KIFC3	ENSG00000140859	-0.437087	0.00e+00	0.00e+00	0	0.264	Malignant cells	NA
TRMT112	ENSG00000173113	-0.437115	0.00e+00	0.00e+00	0.941	0.991	Malignant cells	NA
RAD21	ENSG00000164754	-0.437447	2.73e-36	6.07e-32	0.916	0.968	Malignant cells	NA
KIAA1524	NA	-0.438177	5.52e-20	1.23e-15	0.467	0.559	Malignant cells	NA
MIEN1	ENSG00000141741	-0.438253	2.95e-27	6.56e-23	0.495	0.626	Malignant cells	NA
STAU1	ENSG00000124214	-0.438301	1.78e-25	3.96e-21	0.395	0.539	Malignant cells	NA
TIMELESS	ENSG00000111602	-0.438311	1.30e-30	2.90e-26	0.301	0.473	Malignant cells	NA
BAG2	ENSG00000112208	-0.438316	6.35e-35	1.41e-30	0.589	0.742	Malignant cells	NA
COA4	ENSG00000181924	-0.438389	1.40e-45	4.59e-41	0.807	0.928	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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