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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_Pal

Dataset summary for GSE131984_Pal

Datast information	Dataset	GSE131984_Pal
	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	palbociclib
	Drug type	Targeted therapy
	Sample size	resistant 1, sensitive 2
	Cell number	1754
	Extract protocol	10x genomics
	Data processing	CellRanger 2.1.0
	Public date	Public on Apr 08, 2022
	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_Pal

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"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
SAA1	ENSG00000288411	1.74785	0.00e+00	0.00e+00	0.593	0.199	Malignant cells	NA
FN1	ENSG00000115414	1.5089	0.00e+00	0.00e+00	0.918	0.551	Malignant cells	NA
MT1X	ENSG00000187193	1.4799	0.00e+00	0.00e+00	0.996	0.937	Malignant cells	NA
TGFBI	ENSG00000120708	1.24474	0.00e+00	0.00e+00	0.996	0.907	Malignant cells	NA
MXD4	ENSG00000123933	1.17022	0.00e+00	0.00e+00	0.987	0.85	Malignant cells	NA
NEAT1	ENSG00000245532	1.12888	0.00e+00	0.00e+00	1	0.993	Malignant cells	NA
SOD2	ENSG00000291237	1.104	0.00e+00	0.00e+00	0.997	0.958	Malignant cells	NA
NR4A1	ENSG00000123358	1.08444	0.00e+00	0.00e+00	0.654	0.194	Malignant cells	NA
PNRC1	ENSG00000146278	1.03949	0.00e+00	0.00e+00	0.967	0.724	Malignant cells	NA
IL6	ENSG00000136244	0.898638	0.00e+00	0.00e+00	0.827	0.555	Malignant cells	NA
STAC2	ENSG00000141750	0.893894	0.00e+00	0.00e+00	0.582	0.191	Malignant cells	NA
ASS1	ENSG00000130707	0.892779	0.00e+00	0.00e+00	0.635	0.172	Malignant cells	NA
IL13RA2	ENSG00000123496	0.867792	0.00e+00	0.00e+00	0.439	0.117	Malignant cells	NA
RAMP1	ENSG00000132329	0.850058	0.00e+00	0.00e+00	0.782	0.458	Malignant cells	NA
FTH1	ENSG00000167996	0.822019	0.00e+00	0.00e+00	1	1	Malignant cells	NA
DUSP1	ENSG00000120129	0.821607	0.00e+00	0.00e+00	0.955	0.74	Malignant cells	NA
ABCC3	ENSG00000108846	0.804975	0.00e+00	0.00e+00	0.812	0.495	Malignant cells	NA
MT-CYB	ENSG00000198727	0.769277	0.00e+00	0.00e+00	1	0.999	Malignant cells	NA
MT1E	ENSG00000169715	0.764209	2.08e-35	3.28e-31	0.949	0.877	Malignant cells	NA
ZFP36	ENSG00000128016	0.754257	0.00e+00	0.00e+00	0.833	0.583	Malignant cells	NA
F2R	ENSG00000181104	0.742401	0.00e+00	0.00e+00	0.873	0.666	Malignant cells	NA
MT-CO3	ENSG00000198938	0.737474	0.00e+00	0.00e+00	1	0.999	Malignant cells	NA
FOS	ENSG00000170345	0.715534	2.41e-43	3.81e-39	0.638	0.315	Malignant cells	NA
MT2A	ENSG00000125148	0.695645	0.00e+00	5.71e-42	1	0.997	Malignant cells	NA
MYC	ENSG00000136997	0.695644	0.00e+00	0.00e+00	0.986	0.959	Malignant cells	NA
EGR1	ENSG00000120738	0.682051	0.00e+00	2.80e-45	0.938	0.756	Malignant cells	NA
MT-CO1	ENSG00000198804	0.67814	0.00e+00	0.00e+00	1	0.999	Malignant cells	NA
COL6A2	ENSG00000142173	0.670856	0.00e+00	4.05e-42	0.569	0.253	Malignant cells	NA
FOSB	ENSG00000125740	0.670761	0.00e+00	1.40e-45	0.593	0.254	Malignant cells	NA
SLPI	ENSG00000124107	0.669169	1.40e-45	3.31e-41	0.323	0.066	Malignant cells	NA
MT-ATP6	ENSG00000198899	0.661402	0.00e+00	0.00e+00	1	0.998	Malignant cells	NA
MT-ND4	ENSG00000198886	0.658171	0.00e+00	0.00e+00	1	0.999	Malignant cells	NA
C11orf96	ENSG00000187479	0.648958	2.25e-33	3.56e-29	0.307	0.089	Malignant cells	NA
AQP3	ENSG00000165272	0.631228	3.64e-37	5.75e-33	0.395	0.137	Malignant cells	NA
ITGA3	ENSG00000005884	0.6295	1.40e-45	1.94e-41	0.876	0.668	Malignant cells	NA
DUSP23	ENSG00000158716	0.609472	1.40e-45	1.34e-41	0.984	0.956	Malignant cells	NA
FAM20C	ENSG00000282147	0.601054	0.00e+00	6.70e-42	0.364	0.093	Malignant cells	NA
MCL1	ENSG00000143384	0.593031	2.80e-45	3.76e-41	0.948	0.861	Malignant cells	NA
CPD	ENSG00000108582	0.59013	7.31e-41	1.16e-36	0.566	0.281	Malignant cells	NA
AHNAK2	ENSG00000185567	0.587453	9.54e-33	1.51e-28	0.746	0.528	Malignant cells	NA
ANPEP	ENSG00000166825	0.579907	2.05e-37	3.24e-33	0.916	0.765	Malignant cells	NA
TNFAIP3	ENSG00000118503	0.578908	1.36e-33	2.14e-29	0.733	0.492	Malignant cells	NA
VSTM2L	ENSG00000132821	0.575975	1.29e-38	2.04e-34	0.618	0.322	Malignant cells	NA
LY6E	ENSG00000278032	0.575349	0.00e+00	6.30e-42	0.978	0.937	Malignant cells	NA
FSTL1	ENSG00000163430	0.575316	0.00e+00	0.00e+00	0.492	0.153	Malignant cells	NA
NABP1	ENSG00000173559	0.573461	1.25e-39	1.98e-35	0.576	0.294	Malignant cells	NA
AGRN	ENSG00000188157	0.566644	0.00e+00	0.00e+00	0.528	0.2	Malignant cells	NA
XIST	ENSG00000229807	0.566159	1.22e-26	1.93e-22	0.88	0.8	Malignant cells	NA
MALAT1	ENSG00000251562	0.558848	2.52e-44	3.98e-40	1	1	Malignant cells	NA
CD81	ENSG00000110651	0.557807	8.52e-39	1.35e-34	0.798	0.578	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-16	5.60e-16	1570	781	117	23467	Malignant cells	ABL1,ANXA2,ATG5,AURKA,BAX,BIRC5,CDK4,CIAPIN1,DNMT1,DUSP6,EPAS1,FADD,HIF1A,HMGA1,HMGB1,IL6,PKM,MCL1,MEF2D,MUC1,MYC,PARP1,PDGFRA,RHOA,S100A4,SHC1,STMN1,TGFBR2,PBK,TYMS,VEGFA,SLC25A5,AIFM1,AKAP12,ANXA1,ATG3,BAG1,HSPA5,BRD7,CAV2,CCNA2,CCNB1,CDK1,CCND1,CCNG2,CD44,HSPD1,COL1A1,CSF1,DKK1,DUSP1,DUSP2,EGR1,HSP90B1,ERRFI1,EZH2,EZR,FN1,FOXO3,FUS,GRB2,GCLM,HAX1,HIPK2,HMGB2,HMGN5,HSPA8,EIF4A3,EIF4E,NFKBIA,ITGA5,ITGB1,LDHA,LRRFIP1,MTDH,MXD4,MAGEA3,MYBL2,PIK3R1,PDCD10,PDCD4,PGK1,AGPAT2,PLK1,POMP,PSMB5,RAC1,RAP1B,HRAS,RRM1,RRM2,S100A11,SDHB,SMC4,SOD2,SRSF2,STAT3,TFAM,TNFAIP3,UBE2C,USP22,ZKSCAN1,ENO1,FASN,IDH3A,GNAS,NPM1,CEBPD,EIF4EBP1,IDI1,INSIG1,SQLE,PMVK,EBP,TRIB3,APP,ACAT2
Drug Inactivation by Structure Modification	2.70e-01	6.70e-01	1570	27	3	23467	Malignant cells	SOD2,CDA,NME1
Irregularity in Drug Uptake and Drug Efflux	4.50e-01	7.00e-01	1570	37	3	23467	Malignant cells	SLC3A2,ABCA1,ABCE1
Aberration of the Drug's Therapeutic Target	5.60e-01	7.00e-01	1570	90	6	23467	Malignant cells	ABL1,CDK4,PDGFRA,EZH2,NPM1,MAOA
Epigenetic Alteration of DNA, RNA or Protein	1.00e+00	1.00e+00	1570	455	17	23467	Malignant cells	ABL1,ATG5,DNMT1,H2AFY,IL6,LMNA,TYMS,PMAIP1,EZH2,FOXO3,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
	cisbp__M00161	3.98	0.0839	FOXJ1 (inferredBy_Orthology).	Malignant cells
	metacluster_26.7	3.69	0.0808	MYNN; MYNN (directAnnotation).	Malignant cells
	transfac_pro__M07260	3.63	0.0801	IKZF1 (directAnnotation).	Malignant cells
	taipale_tf_pairs__HOXB13_ONECUT2_NNNRTAAAWATYGAYY_CAP	3.59	0.0796	HOXB13; ONECUT2 (directAnnotation).	Malignant cells
	transfac_pro__M05462	3.52	0.0789	ZNF581 (directAnnotation).	Malignant cells
	transfac_pro__M01835	3.45	0.0781	KLF4 (directAnnotation).	Malignant cells
	jaspar__MA1125.1	3.42	0.0778	ZNF384 (directAnnotation).	Malignant cells
	metacluster_134.7	3.4	0.0775	FOXD2; FOXG1; FOXI1; FOXJ2; FOXJ2; FOXJ3; FOXJ3; FOXK1; FOXK1; FOXK2; FOXO4; FOXO6; FOXP2 (directAnnotation). FOXC1; FOXO1; FOXO6 (inferredBy_Orthology).	Malignant cells
	metacluster_127.2	3.35	0.077	FOXA1; FOXA2; FOXA3; FOXC1; FOXC1; FOXC2; FOXD1; FOXD1; FOXF2; FOXF2; FOXJ1; FOXK2; FOXK2; FOXO6; FOXP1; FOXP1; FOXP1; FOXP1 (directAnnotation). FOXD2; FOXF1; FOXL3; FOXO1; FOXO3 (inferredBy_Orthology).	Malignant cells
	kznf__ZNF613_Imbeault2017_RP_RCADE	3.34	0.0769	ZNF613 (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	7.55	0.0658	ETS2 (directAnnotation).	Malignant cells
	metacluster_191.3	6.55	0.06	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
	transfac_pro__M04826	6.35	0.0589	EP300 (directAnnotation).	Malignant cells
	taipale_tf_pairs__ETV5_HOXA2_RSCGGWAATKR_CAP	6.1	0.0574	ETV5; HOXA2 (directAnnotation).	Malignant cells
	metacluster_166.4	6.01	0.0569	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	5.96	0.0566	ELK4; NR2C2; NR2C2; NR2C2; NR2C2 (directAnnotation). GABPA (inferredBy_Orthology).	Malignant cells
	taipale_tf_pairs__ELK1_HOXA1_RCCGGAAGTAATTA_HT	5.55	0.0542	ELK1; HOXA1 (directAnnotation).	Malignant cells
	taipale_tf_pairs__MEIS1_ELF1_NTGCCGGAAGTN_CAP_repr	5.51	0.054	ELF1; MEIS1 (directAnnotation).	Malignant cells
	taipale_tf_pairs__FOXO1_ELK3_RCCGGAWGTKKW_CAP	5.5	0.0539	ELK3; FOXO1 (directAnnotation).	Malignant cells
	metacluster_166.2	5.36	0.0531	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
ETV1	metacluster_191.3	up	Malignant cells	NA
ETV1	metacluster_166.4	up	Malignant cells	NA
ETV1	metacluster_166.2	up	Malignant cells	NA
FOS	metacluster_174.2	up	Malignant cells	NA
ETV1	metacluster_138.2	up	Malignant cells	NA
ETV1	taipale_tf_pairs__HOXB2_ETV1_ACCGGAAATGA_CAP	up	Malignant cells	NA
ETV1	taipale_tf_pairs__TEAD4_ETV1_RSCGGAAATRCM_CAP	up	Malignant cells	NA
EGR1	metacluster_55.3	up	Malignant cells	NA
EGR1	metacluster_34.3	up	Malignant cells	NA
ZNF581	transfac_pro__M05462	up	Malignant cells	NA

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