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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_JQ1Pac

Dataset summary for GSE131984_JQ1Pac

Datast information	Dataset	GSE131984_JQ1Pac
	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 + paclitaxel
	Drug type	Targeted therapy
	Sample size	resistant 1, sensitive 2
	Cell number	1704
	Extract protocol	10x genomics
	Data processing	CellRanger 2.1.0
	Public date	Public on Apr 08, 2023
	Description	This dataset has 1 cell line with 2 sensitive pre-treatment samples and 1 resistant post-treatment sample.

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Drug summary for GSE131984_JQ1Pac

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"JQ1" is not included in the drug list.
"Paclitaxel"	DB01229	small molecule	TUBB1; BCL2; MAP4; MAP2; MAPT; NR1I2	Q9H4B7; P10415; P27816; P11137; P10636; O75469

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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
FABP4	ENSG00000170323	2.49063	0.00e+00	0.00e+00	0.358	0.015	Malignant cells	NA
HCFC1R1	ENSG00000103145	1.40865	0.00e+00	0.00e+00	0.958	0.721	Malignant cells	NA
VSTM2L	ENSG00000132821	1.28924	0.00e+00	0.00e+00	0.826	0.319	Malignant cells	NA
MALAT1	ENSG00000251562	1.26066	0.00e+00	0.00e+00	1	1	Malignant cells	NA
PEG10	ENSG00000242265	1.22538	0.00e+00	0.00e+00	0.862	0.563	Malignant cells	NA
MT1X	ENSG00000187193	1.22466	8.62e-33	1.33e-28	0.958	0.936	Malignant cells	NA
TGFBI	ENSG00000120708	1.20789	0.00e+00	0.00e+00	0.983	0.897	Malignant cells	NA
STAC2	ENSG00000141750	1.17364	0.00e+00	0.00e+00	0.602	0.188	Malignant cells	NA
FN1	ENSG00000115414	1.09597	0.00e+00	0.00e+00	0.877	0.549	Malignant cells	NA
FTL	ENSG00000087086	1.04686	0.00e+00	0.00e+00	1	1	Malignant cells	NA
GPX4	ENSG00000167468	0.961516	0.00e+00	0.00e+00	1	1	Malignant cells	NA
MYC	ENSG00000136997	0.926969	0.00e+00	0.00e+00	0.991	0.952	Malignant cells	NA
CIRBP	ENSG00000099622	0.905793	0.00e+00	0.00e+00	0.997	0.95	Malignant cells	NA
RAMP1	ENSG00000132329	0.871313	0.00e+00	0.00e+00	0.762	0.453	Malignant cells	NA
FTH1	ENSG00000167996	0.863025	0.00e+00	0.00e+00	1	1	Malignant cells	NA
MMP24-AS1	NA	0.794573	0.00e+00	0.00e+00	0.994	0.938	Malignant cells	NA
C9orf16	NA	0.792009	0.00e+00	0.00e+00	0.998	0.978	Malignant cells	NA
MXD4	ENSG00000123933	0.787836	0.00e+00	1.40e-45	0.947	0.837	Malignant cells	NA
NEAT1	ENSG00000245532	0.743629	5.02e-36	7.73e-32	1	0.992	Malignant cells	NA
GAPDH	ENSG00000111640	0.742197	0.00e+00	0.00e+00	1	1	Malignant cells	NA
SEPP1	NA	0.739675	4.46e-29	6.88e-25	0.474	0.238	Malignant cells	NA
TXNIP	ENSG00000265972	0.702445	1.11e-31	1.72e-27	0.46	0.218	Malignant cells	NA
TTC3	ENSG00000182670	0.694887	0.00e+00	0.00e+00	0.944	0.785	Malignant cells	NA
PHPT1	ENSG00000054148	0.688898	0.00e+00	0.00e+00	0.984	0.917	Malignant cells	NA
CITED2	ENSG00000164442	0.685416	5.97e-42	9.20e-38	0.743	0.47	Malignant cells	NA
TMPRSS15	ENSG00000154646	0.676023	0.00e+00	2.19e-43	0.826	0.628	Malignant cells	NA
CCDC85B	ENSG00000175602	0.671857	1.50e-40	2.32e-36	0.994	0.989	Malignant cells	NA
MT2A	ENSG00000125148	0.665898	2.33e-28	3.59e-24	1	0.997	Malignant cells	NA
ASS1	ENSG00000130707	0.663733	6.09e-41	9.39e-37	0.451	0.172	Malignant cells	NA
TPT1	ENSG00000133112	0.641404	0.00e+00	0.00e+00	1	1	Malignant cells	NA
RNASEH2C	ENSG00000172922	0.636574	0.00e+00	0.00e+00	0.927	0.784	Malignant cells	NA
RPL22L1	ENSG00000163584	0.629648	1.33e-17	2.05e-13	0.989	0.995	Malignant cells	NA
GNAS	ENSG00000087460	0.619871	0.00e+00	0.00e+00	0.97	0.886	Malignant cells	NA
RPL28	ENSG00000108107	0.619295	0.00e+00	0.00e+00	1	1	Malignant cells	NA
COMMD6	ENSG00000188243	0.617167	0.00e+00	0.00e+00	0.983	0.944	Malignant cells	NA
NQO1	ENSG00000181019	0.616614	9.20e-28	1.42e-23	0.991	0.974	Malignant cells	NA
TXNRD1	ENSG00000198431	0.61243	3.65e-35	5.63e-31	0.966	0.926	Malignant cells	NA
ZFAS1	ENSG00000177410	0.606817	0.00e+00	0.00e+00	1	1	Malignant cells	NA
ZFP36	ENSG00000128016	0.602015	1.18e-32	1.82e-28	0.798	0.576	Malignant cells	NA
NR4A1	ENSG00000123358	0.594355	6.00e-26	9.25e-22	0.417	0.2	Malignant cells	NA
DCXR	ENSG00000169738	0.583001	6.24e-42	9.62e-38	0.953	0.926	Malignant cells	NA
ITFG3	NA	0.580411	0.00e+00	1.99e-43	0.6	0.289	Malignant cells	NA
GAMT	ENSG00000130005	0.57755	1.27e-25	1.95e-21	0.561	0.344	Malignant cells	NA
ITGA3	ENSG00000005884	0.577035	1.61e-33	2.48e-29	0.834	0.665	Malignant cells	NA
LAGE3	ENSG00000196976	0.570252	1.15e-41	1.78e-37	0.981	0.926	Malignant cells	NA
FSTL1	ENSG00000163430	0.554885	6.87e-44	1.05e-39	0.449	0.153	Malignant cells	NA
IRX2	ENSG00000170561	0.550904	3.34e-38	5.14e-34	1	0.997	Malignant cells	NA
ID1	ENSG00000125968	0.54799	1.61e-18	2.49e-14	0.882	0.787	Malignant cells	NA
CD33	ENSG00000105383	0.543651	0.00e+00	0.00e+00	0.473	0.146	Malignant cells	NA
TMSB10	ENSG00000034510	0.519273	0.00e+00	0.00e+00	1	1	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-16	1.70e-15	1949	781	134	23467	Malignant cells	ATG5,AURKA,BAX,BCAT1,BIRC5,CTSL,CDCP1,CDK4,CDKN1A,CERS2,CFLAR,CIAPIN1,DCTD,FADD,HMGA1,HMGB1,ID1,IFI27,IL6,ISG15,MAGEA6,MAGEA12,MCL1,MYC,PDGFRA,PPARG,SHC1,ST3GAL4,SOX4,SOX9,SPRY2,STMN1,TGFB1,PBK,TYMS,VOPP1,XIAP,SLC25A5,AIFM1,AKAP12,AR,ANXA1,ATG3,BAD,BAG1,BID,HSPA5,BRD7,CASP1,CAV2,CCNA2,CCNB1,CDK1,HSPD1,COL1A1,CRIM1,DKK1,EGR1,EIF3A,HSP90B1,EZH2,EZR,FN1,FTL,GAPDH,G6PD,GAS6,GRB2,GCLM,HAX1,HMGN5,HNRNPU,EIF4A3,EIF4E,NFKBIA,IL18,KLF4,RPS6KA3,LAMP2,LDHA,LRRFIP1,MTDH,MXD4,MAGEA3,MAPK3,MAP2K2,MYBL2,IKBKG,NQO1,PIK3R1,PDCD10,PGK1,AGPAT2,PLK1,POMP,PSMB5,RAP1B,HRAS,NRAS,RAB27A,RRM1,RND3,S100A11,SDHB,SIAH2,SMC4,SOD2,SRSF2,TPT1,TFAM,TMED3,TNFAIP3,YY1,UBE2C,AXL,WLS,ENO1,IDH3A,GNAS,CD33,ARAF,NPM1,IL7R,EIF4EBP1,IDI1,RCN1,RELB,SQLE,PMVK,EBP,NUPR1,TRIB3,WTAP,ACAT2
Irregularity in Drug Uptake and Drug Efflux	8.20e-02	2.10e-01	1949	37	6	23467	Malignant cells	SLC3A2,ABCF2,ABCE1,SLC7A5,TAP1,SLC7A11
Drug Inactivation by Structure Modification	1.80e-01	3.00e-01	1949	27	4	23467	Malignant cells	CES1,SOD2,CDA,NME1
Aberration of the Drug's Therapeutic Target	4.70e-01	5.90e-01	1949	90	8	23467	Malignant cells	CDK4,PDGFRA,AR,EZH2,MAP2K2,NPM1,COMT,AKR1B1
Epigenetic Alteration of DNA, RNA or Protein	1.00e+00	1.00e+00	1949	455	17	23467	Malignant cells	ATG5,H2AFY,IL6,PPARG,SPRY2,TRIP6,TYMS,XIAP,PMAIP1,EZH2,GAPDH,MAPK3,SMC4,TIMP1,MALAT1,GDI2,PPP1R15A

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
	transfac_pro__M05993	4.65	0.0734	ZNF711 (directAnnotation).	Malignant cells
	hocomoco__FOXP1_HUMAN.H11MO.0.A	4.35	0.0706	FOXP1 (directAnnotation).	Malignant cells
	metacluster_22.16	4.22	0.0692	BACH2 (directAnnotation).	Malignant cells
	metacluster_22.12	4.15	0.0686	NFE2; NFE2L1 (directAnnotation).	Malignant cells
	metacluster_22.25	4.07	0.0678	NFE2L2 (directAnnotation).	Malignant cells
	metacluster_22.13	3.97	0.0668	MAFK (inferredBy_Orthology).	Malignant cells
	metacluster_22.17	3.84	0.0655	NFE2 (directAnnotation).	Malignant cells
	metacluster_22.11	3.83	0.0655	NFE2 (directAnnotation).	Malignant cells
	metacluster_22.19	3.83	0.0654	NFE2 (directAnnotation).	Malignant cells
	metacluster_22.20	3.8	0.0651	MAFG (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
	taipale_tf_pairs__ETS2_RCCGGAAGTG_HT	7.25	0.0649	ETS2 (directAnnotation).	Malignant cells
	metacluster_191.3	6.86	0.0627	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	6.4	0.0601	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
	metacluster_191.2	6.15	0.0587	ELK4; NR2C2; NR2C2; NR2C2; NR2C2 (directAnnotation). GABPA (inferredBy_Orthology).	Malignant cells
	taipale_tf_pairs__FOXO1_ELK3_RCCGGAWGTKKW_CAP	5.99	0.0577	ELK3; FOXO1 (directAnnotation).	Malignant cells
	taipale_tf_pairs__ETV5_HOXA2_RSCGGWAATKR_CAP	5.73	0.0563	ETV5; HOXA2 (directAnnotation).	Malignant cells
	jaspar__MA1483.2	5.62	0.0557	ELF2 (directAnnotation).	Malignant cells
	metacluster_166.2	5.52	0.0551	ELK4; ETS1; ETS1; ETV1; ETV3; ETV4; ETV5; ETV7 (directAnnotation). GABPA (inferredBy_Orthology).	Malignant cells
	transfac_pro__M04826	5.32	0.054	EP300 (directAnnotation).	Malignant cells
	taipale_tf_pairs__MEIS1_ELF1_NTGCCGGAAGTN_CAP_repr	5.3	0.0538	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
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
ETV4	metacluster_166.4	down	Malignant cells	NA
ETV4	metacluster_166.2	down	Malignant cells	NA
ETS2	metacluster_138.2	down	Malignant cells	NA
ETV4	metacluster_138.2	down	Malignant cells	NA
ETV4	hdpi__ETV4	down	Malignant cells	NA
ZNF385D	taipale_cyt_meth__ZNF385D_NCGTCGCGACGN_eDBD_meth	down	Malignant cells	NA
ETV4	taipale_tf_pairs__HOXB2_ETV4_ACCGGAAATGAN_CAP	down	Malignant cells	NA

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