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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
ITFG3	NA	0.628201	0.00e+00	0.00e+00	0.635	0.287	Malignant cells	NA
RP11-545E17.3	NA	0.617754	0.00e+00	0.00e+00	0.695	0.352	Malignant cells	NA
TAF10	ENSG00000166337	0.61696	0.00e+00	0.00e+00	0.975	0.858	Malignant cells	NA
IRX2	ENSG00000170561	0.616373	0.00e+00	0.00e+00	1	0.997	Malignant cells	NA
AMOTL2	ENSG00000114019	0.610636	0.00e+00	0.00e+00	0.542	0.219	Malignant cells	NA
PYGB	ENSG00000100994	0.608433	0.00e+00	0.00e+00	0.84	0.573	Malignant cells	NA
ITGB5	ENSG00000082781	0.608239	0.00e+00	0.00e+00	0.71	0.412	Malignant cells	NA
Z83851.1	NA	0.60591	0.00e+00	0.00e+00	0.386	0.025	Malignant cells	NA
MT1E	ENSG00000169715	0.592692	2.90e-27	4.58e-23	0.925	0.879	Malignant cells	NA
STX16	ENSG00000124222	0.5906	0.00e+00	0.00e+00	0.652	0.348	Malignant cells	NA
OSBPL5	ENSG00000021762	0.588918	0.00e+00	0.00e+00	0.493	0.127	Malignant cells	NA
F2R	ENSG00000181104	0.588621	0.00e+00	0.00e+00	0.876	0.666	Malignant cells	NA
RAPH1	ENSG00000173166	0.588511	0.00e+00	0.00e+00	0.577	0.225	Malignant cells	NA
PTRF	NA	0.57838	0.00e+00	0.00e+00	0.945	0.776	Malignant cells	NA
SERPINE2	ENSG00000135919	0.576408	8.36e-42	1.32e-37	0.698	0.438	Malignant cells	NA
MGEA5	NA	0.573436	0.00e+00	0.00e+00	0.739	0.444	Malignant cells	NA
ARPC1B	ENSG00000130429	0.572531	0.00e+00	0.00e+00	0.996	0.99	Malignant cells	NA
CADM3	ENSG00000162706	0.570312	0.00e+00	0.00e+00	0.341	0.035	Malignant cells	NA
BEST1	ENSG00000167995	0.569986	0.00e+00	0.00e+00	0.602	0.256	Malignant cells	NA
TMSB10	ENSG00000034510	0.569672	0.00e+00	0.00e+00	1	1	Malignant cells	NA
AHNAK	ENSG00000124942	0.56895	0.00e+00	0.00e+00	0.998	0.961	Malignant cells	NA
PNPLA2	ENSG00000177666	0.56857	0.00e+00	0.00e+00	0.647	0.365	Malignant cells	NA
EPHA2	ENSG00000142627	0.56645	0.00e+00	8.41e-45	0.607	0.32	Malignant cells	NA
DCBLD2	ENSG00000057019	0.561335	9.81e-44	1.55e-39	0.696	0.459	Malignant cells	NA
RPLP1	ENSG00000137818	0.555881	0.00e+00	0.00e+00	1	1	Malignant cells	NA
HCFC1R1	ENSG00000103145	0.554864	4.90e-36	7.74e-32	0.861	0.734	Malignant cells	NA
COL5A1	ENSG00000130635	0.54725	2.80e-45	5.08e-41	0.61	0.336	Malignant cells	NA
FAM115A	NA	0.546491	0.00e+00	0.00e+00	0.724	0.431	Malignant cells	NA
NSMF	ENSG00000165802	0.546462	0.00e+00	0.00e+00	0.71	0.428	Malignant cells	NA
NR4A1	ENSG00000123358	0.545473	1.41e-29	2.23e-25	0.413	0.201	Malignant cells	NA
RXRA	ENSG00000186350	0.544993	0.00e+00	0.00e+00	0.568	0.247	Malignant cells	NA
SLC20A1	ENSG00000144136	0.54196	7.48e-32	1.18e-27	0.807	0.615	Malignant cells	NA
TGOLN2	ENSG00000152291	0.541676	7.01e-45	1.14e-40	0.79	0.583	Malignant cells	NA
PTTG1IP	ENSG00000183255	0.541211	0.00e+00	0.00e+00	0.687	0.406	Malignant cells	NA
HMOX1	ENSG00000100292	0.538932	4.38e-40	6.93e-36	0.856	0.644	Malignant cells	NA
CRIP2	ENSG00000182809	0.538336	1.69e-39	2.68e-35	0.523	0.265	Malignant cells	NA
RPL12	ENSG00000197958	0.535295	0.00e+00	0.00e+00	1	1	Malignant cells	NA
METRN	ENSG00000103260	0.534482	1.40e-45	2.26e-41	0.949	0.871	Malignant cells	NA
TP53I3	ENSG00000115129	0.534069	0.00e+00	9.81e-45	0.529	0.236	Malignant cells	NA
DUSP6	ENSG00000139318	0.533709	4.18e-32	6.61e-28	0.683	0.472	Malignant cells	NA
NRCAM	ENSG00000091129	0.531226	0.00e+00	0.00e+00	0.407	0.07	Malignant cells	NA
BCL2L1	ENSG00000171552	0.530144	2.21e-37	3.49e-33	0.788	0.593	Malignant cells	NA
DCXR	ENSG00000169738	0.525996	1.40e-45	1.67e-41	0.967	0.93	Malignant cells	NA
WEE1	ENSG00000166483	0.525552	3.08e-39	4.87e-35	0.639	0.395	Malignant cells	NA
SH2B3	ENSG00000111252	0.525177	2.97e-41	4.69e-37	0.6	0.338	Malignant cells	NA
GLG1	ENSG00000090863	0.520855	0.00e+00	0.00e+00	0.61	0.314	Malignant cells	NA
NME3	ENSG00000103024	0.519835	9.77e-43	1.54e-38	0.829	0.616	Malignant cells	NA
CIRBP	ENSG00000099622	0.519801	0.00e+00	0.00e+00	0.988	0.959	Malignant cells	NA
ACYP2	ENSG00000170634	0.517057	0.00e+00	0.00e+00	0.533	0.239	Malignant cells	NA
KIF5C	ENSG00000276734	0.516145	0.00e+00	0.00e+00	0.331	0.029	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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