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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: GSE131984_JQ1Pal

Dataset summary for GSE131984_JQ1Pal

Datast information	Dataset	GSE131984_JQ1Pal
	PMID	32393766
	Raw data ID/link	PRJNA545508
	Organism	Homo sapiens
	Source	SUM159 cell line
	Tissue	Cell line
	Cancer type level1	Breast cancer
	Cancer type level2	Triple-negative breast cancer (TNBC)
	Regimen	JQ1 + palbociclib
	Drug type	Targeted therapy
	Sample size	resistant 1, sensitive 2
	Cell number	2085
	Extract protocol	10x genomics
	Data processing	CellRanger 2.1.0
	Public date	Public on Apr 08, 2024
	Description	This dataset has 1 cell line with 2 sensitive pre-treatment samples and 1 resistant post-treatment samples.

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Drug summary for GSE131984_JQ1Pal

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"JQ1" is not included in the drug list.
"Palbociclib"	DB09073	small molecule	CDK4; CDK6	P11802; Q00534

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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
ACBD6	ENSG00000230124	-0.393093	2.34e-27	3.70e-23	0.567	0.727	Malignant cells	NA
MLF2	ENSG00000089693	-0.393227	2.68e-35	4.24e-31	0.87	0.946	Malignant cells	NA
BCCIP	ENSG00000107949	-0.393304	5.07e-25	8.02e-21	0.45	0.643	Malignant cells	NA
C20orf24	NA	-0.393342	5.18e-34	8.19e-30	0.851	0.925	Malignant cells	NA
WLS	ENSG00000116729	-0.393536	2.04e-28	3.23e-24	0.345	0.559	Malignant cells	NA
TCEA1	ENSG00000187735	-0.393982	1.88e-34	2.97e-30	0.819	0.915	Malignant cells	NA
SSBP1	ENSG00000262771	-0.394024	8.47e-34	1.34e-29	0.975	0.993	Malignant cells	NA
PACSIN3	ENSG00000165912	-0.394491	0.00e+00	0.00e+00	0.066	0.33	Malignant cells	NA
APOPT1	NA	-0.394653	8.61e-28	1.36e-23	0.606	0.77	Malignant cells	NA
ITGAE	ENSG00000083457	-0.395091	8.80e-29	1.39e-24	0.841	0.908	Malignant cells	NA
CBR1	ENSG00000159228	-0.395302	8.53e-38	1.35e-33	0.885	0.963	Malignant cells	NA
PAIP1	ENSG00000172239	-0.395427	2.45e-29	3.87e-25	0.765	0.867	Malignant cells	NA
GNG11	ENSG00000127920	-0.395432	9.35e-24	1.48e-19	0.979	0.982	Malignant cells	NA
TMEM11	ENSG00000178307	-0.396485	7.14e-25	1.13e-20	0.414	0.604	Malignant cells	NA
BCAT1	ENSG00000060982	-0.396585	5.22e-29	8.25e-25	0.476	0.674	Malignant cells	NA
FBXO7	ENSG00000100225	-0.3966	2.85e-29	4.50e-25	0.561	0.732	Malignant cells	NA
TAF7	ENSG00000178913	-0.39672	3.27e-24	5.17e-20	0.402	0.598	Malignant cells	NA
SHMT2	ENSG00000182199	-0.396868	2.81e-23	4.45e-19	0.524	0.681	Malignant cells	NA
TPM3	ENSG00000143549	-0.397086	1.70e-37	2.69e-33	0.94	0.976	Malignant cells	NA
PELO	ENSG00000152684	-0.397584	1.46e-26	2.31e-22	0.424	0.625	Malignant cells	NA
COA4	ENSG00000181924	-0.398076	6.43e-35	1.02e-30	0.892	0.958	Malignant cells	NA
TPM1	ENSG00000140416	-0.398167	4.90e-29	7.75e-25	0.959	0.977	Malignant cells	NA
COMMD3	ENSG00000148444	-0.398438	1.41e-28	2.23e-24	0.574	0.748	Malignant cells	NA
NUF2	ENSG00000143228	-0.398693	1.94e-23	3.07e-19	0.184	0.371	Malignant cells	NA
SRSF4	ENSG00000116350	-0.398721	7.22e-30	1.14e-25	0.507	0.711	Malignant cells	NA
CD47	ENSG00000196776	-0.399438	1.45e-27	2.29e-23	0.664	0.827	Malignant cells	NA
COPS8	ENSG00000198612	-0.399478	9.42e-27	1.49e-22	0.75	0.854	Malignant cells	NA
ENDOG	ENSG00000167136	-0.399496	2.50e-29	3.94e-25	0.41	0.62	Malignant cells	NA
CHORDC1	ENSG00000285023	-0.399839	5.84e-30	9.22e-26	0.248	0.477	Malignant cells	NA
C12orf45	NA	-0.40008	1.88e-24	2.98e-20	0.521	0.694	Malignant cells	NA
RSL24D1	ENSG00000137876	-0.400089	2.09e-37	3.30e-33	0.935	0.978	Malignant cells	NA
C12orf10	NA	-0.400383	1.23e-28	1.94e-24	0.653	0.806	Malignant cells	NA
SNORA76	NA	-0.400388	1.85e-17	2.92e-13	0.783	0.836	Malignant cells	NA
JUN	ENSG00000177606	-0.400437	9.17e-10	1.45e-05	0.329	0.437	Malignant cells	NA
DGUOK	ENSG00000114956	-0.400498	4.00e-40	6.32e-36	0.932	0.98	Malignant cells	NA
FAM192A	NA	-0.401201	2.70e-29	4.26e-25	0.423	0.635	Malignant cells	NA
CEBPD	ENSG00000221869	-0.401318	2.98e-17	4.72e-13	0.85	0.894	Malignant cells	NA
ZNF259	NA	-0.401604	9.01e-27	1.42e-22	0.512	0.683	Malignant cells	NA
CYB5B	ENSG00000103018	-0.401871	5.35e-23	8.45e-19	0.479	0.643	Malignant cells	NA
POLR1D	ENSG00000186184	-0.401879	6.17e-44	9.64e-40	0.998	0.999	Malignant cells	NA
PSMD13	ENSG00000185627	-0.402035	3.45e-24	5.45e-20	0.59	0.728	Malignant cells	NA
EWSR1	ENSG00000182944	-0.402081	1.39e-26	2.20e-22	0.688	0.812	Malignant cells	NA
SORBS2	ENSG00000154556	-0.402088	8.39e-25	1.33e-20	0.25	0.453	Malignant cells	NA
MTCH1	ENSG00000137409	-0.402325	1.79e-35	2.82e-31	0.868	0.936	Malignant cells	NA
BTF3	ENSG00000145741	-0.402348	0.00e+00	0.00e+00	1	1	Malignant cells	NA
ZC3H13	ENSG00000123200	-0.402686	2.22e-28	3.51e-24	0.438	0.649	Malignant cells	NA
MRPL2	ENSG00000112651	-0.402937	1.72e-31	2.72e-27	0.294	0.524	Malignant cells	NA
RAP1B	ENSG00000127314	-0.403087	4.62e-29	7.30e-25	0.728	0.83	Malignant cells	NA
PCNP	ENSG00000081154	-0.403182	1.42e-32	2.24e-28	0.822	0.897	Malignant cells	NA
CCAT1	NA	-0.403328	3.75e-18	5.93e-14	0.246	0.404	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	3.30e-23	1.70e-22	2427	781	174	23467	Malignant cells	ADAM10,ATG5,AURKA,BAX,BBC3,BCAT1,BIRC5,CTSL,CDCP1,CDK4,CFLAR,CIAPIN1,DCTD,DUSP6,EGFR,EPAS1,FADD,FBXW7,FUBP1,GLS,HMGA1,HMGB1,HMOX1,IFI27,ISG15,JUN,MAGEA6,MAGEA12,MCL1,MET,MYC,PARP1,PPARG,RHOA,S100A4,SHC1,SOX4,SOX9,SPRY2,STMN1,TGFB1,TGFBR2,PBK,TYMS,AAMDC,SLC25A5,AIFM1,AR,ANXA1,TFAP2A,ATG3,ATM,BID,HSPA5,BRD7,CASP1,CAV2,CCNA2,CCNB1,CDK1,CCND1,CD44,HSPD1,COL1A1,CRIM1,CUL4A,DDIT3,HSP90B1,EPHA2,EREG,EZH2,EZR,FAT1,FN1,FIS1,FOXO3,FTL,FUS,FYN,G6PD,GAS6,GRB2,HAX1,HDAC3,HIPK2,HMGB2,HMGN5,HNRNPU,HSPA8,HSPB1,EIF4A1,EIF4A3,EIF4E,NFKBIA,ITGB1,LASP1,LDHA,LRRFIP1,MTDH,MXD4,MAGEA3,MAPK3,MYBL2,NCOA3,NQO1,NUCKS1,PIK3R1,PDCD10,PDCD4,PGK1,AGPAT2,PLK1,POMP,PSMB5,PSMG2,PTPN1,PTPN12,RAP1A,RAP1B,RAB27A,RRM2,HNRNPA1,ROCK2,S100A11,SDC2,SDHB,SFPQ,SMAD7,SMC4,SMUG1,SOCS3,SOD2,SPIN1,SRSF2,STK4,TFAM,TNFAIP3,TUSC3,UBE2C,USP22,AXL,ULK1,WEE1,WLS,XRCC4,YBX1,ZKSCAN1,ZNF217,ENO1,FASN,PFKL,GNAS,CD33,GNA11,GNAQ,ARAF,NPM1,IL7R,CEBPD,EIF4EBP1,EPHB4,IDI1,INSIG1,PRKCA,RCN1,PMVK,EBP,ACAP2,NUPR1,TRIB3,CERS6,APP,WTAP,ACAT2
Drug Inactivation by Structure Modification	1.40e-01	3.50e-01	2427	27	5	23467	Malignant cells	CES1,SOD2,CDA,NME1,CMPK1
Irregularity in Drug Uptake and Drug Efflux	5.40e-01	7.40e-01	2427	37	4	23467	Malignant cells	SLC3A2,ABCA1,ABCE1,TAP1
Aberration of the Drug's Therapeutic Target	5.90e-01	7.40e-01	2427	90	9	23467	Malignant cells	CDK4,EGFR,MET,AR,EZH2,GNA11,NPM1,COMT,AKR1B1
Epigenetic Alteration of DNA, RNA or Protein	1.00e+00	1.00e+00	2427	455	21	23467	Malignant cells	ATG5,EGFR,FBXW7,H2AFY,LMNA,MET,PPARG,SPRY2,TRIP6,TYMS,PMAIP1,EZH2,FOXO3,MAPK3,PDCD4,SMC4,MALAT1,GDI2,PPP1R15A,MT-CO2,NABP1

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__MA0079.5	3.43	0.0646	SP1 (directAnnotation).	Malignant cells
	kznf__KLF1_Barrera2016.2_PBM	3.4	0.0644	KLF1 (directAnnotation).	Malignant cells
	taipale_cyt_meth__ZNF460_NAACGCCCCCCGN_eDBD_repr	3.35	0.064	ZNF460 (directAnnotation).	Malignant cells
	transfac_pro__M05791	3.34	0.0639	ZNF517 (directAnnotation).	Malignant cells
	transfac_pro__M01253	3.32	0.0638	CNOT3 (directAnnotation).	Malignant cells
	hdpi__NFIX	3.3	0.0636	NFIX (directAnnotation).	Malignant cells
	metacluster_134.7	3.27	0.0634	FOXD2; FOXG1; FOXI1; FOXJ2; FOXJ2; FOXJ3; FOXJ3; FOXK1; FOXK1; FOXK2; FOXO4; FOXO6; FOXP2 (directAnnotation). FOXC1; FOXO1; FOXO6 (inferredBy_Orthology).	Malignant cells
	metacluster_153.4	3.12	0.0622	SOX12; SOX14; SRY (directAnnotation). SOX5 (inferredBy_Orthology).	Malignant cells
	transfac_pro__M04817	3.11	0.0621	ZBTB33 (directAnnotation).	Malignant cells
	transfac_pro__M02896	3.07	0.0618	SPI1 (inferredBy_Orthology).	Malignant cells

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Motifs and TFs regulating down-regulated DEGs in resistant group

motif	motif	NES	AUC	TF_highConf	Cell_type
	taipale_tf_pairs__ETS2_RCCGGAAGTG_HT	6.63	0.0607	ETS2 (directAnnotation).	Malignant cells
	metacluster_191.3	6.45	0.0596	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
	metacluster_166.4	6.15	0.0579	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
	transfac_pro__M04826	5.71	0.0554	EP300 (directAnnotation).	Malignant cells
	taipale_tf_pairs__ETV5_HOXA2_RSCGGWAATKR_CAP	5.56	0.0545	ETV5; HOXA2 (directAnnotation).	Malignant cells
	taipale_tf_pairs__FOXO1_ELK3_RCCGGAWGTKKW_CAP	5.45	0.0539	ELK3; FOXO1 (directAnnotation).	Malignant cells
	metacluster_191.2	5.45	0.0539	ELK4; NR2C2; NR2C2; NR2C2; NR2C2 (directAnnotation). GABPA (inferredBy_Orthology).	Malignant cells
	jaspar__MA1483.2	5.32	0.0531	ELF2 (directAnnotation).	Malignant cells
	metacluster_166.2	5.32	0.0531	ELK4; ETS1; ETS1; ETV1; ETV3; ETV4; ETV5; ETV7 (directAnnotation). GABPA (inferredBy_Orthology).	Malignant cells
	taipale_tf_pairs__MEIS1_ELF1_NTGCCGGAAGTN_CAP_repr	5.12	0.052	ELF1; MEIS1 (directAnnotation).	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
ETV1	metacluster_191.3	up	Malignant cells	NA
ETV1	metacluster_166.4	up	Malignant cells	NA
ETV1	metacluster_166.2	up	Malignant cells	NA
ETV1	metacluster_138.2	up	Malignant cells	NA
ETV1	taipale_tf_pairs__TEAD4_ETV1_RSCGGAAATRCM_CAP	up	Malignant cells	NA
STAT1	transfac_pro__M00492	up	Malignant cells	NA
NFIX	hdpi__NFIX	up	Malignant cells	NA
ETS2	taipale_tf_pairs__ETS2_RCCGGAAGTG_HT	down	Malignant cells	NA
ETS2	metacluster_191.3	down	Malignant cells	NA
ETV4	metacluster_191.3	down	Malignant cells	NA

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