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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: GSE139386

Dataset summary for GSE139386

Datast information	Dataset	GSE139386
	PMID	35999456
	Raw data ID/link	PRJNA321747
	Organism	Homo sapiens
	Source	H3122 cell line
	Tissue	Cell line
	Cancer type level1	Lung cancer
	Cancer type level2	EML4-ALK fusion-positive non-small cell lung cancer (NSCLC)
	Regimen	ceritinib
	Drug type	Targeted therapy
	Sample size	resistant 1, sensitive 1
	Cell number	6986
	Extract protocol	10x genomics
	Data processing	CellRanger
	Public date	Public on Sep 20, 2022
	Description	This dataset has 1 cell line with a sensitive pre-treatment sample and a resistant post-treatment sample.

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Drug summary for GSE139386

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"Ceritinib"	DB09063	small molecule	ALK	Q9UM73

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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
MRPL10	ENSG00000159111	0.343158	0.00e+00	0.00e+00	0.593	0.438	Malignant cells	NA
AUP1	ENSG00000115307	0.342766	0.00e+00	0.00e+00	0.899	0.843	Malignant cells	NA
FXYD5	ENSG00000089327	0.342413	0.00e+00	0.00e+00	0.82	0.704	Malignant cells	NA
RASD1	ENSG00000108551	0.342031	0.00e+00	0.00e+00	0.268	0.061	Malignant cells	NA
CALCOCO2	ENSG00000136436	0.341596	0.00e+00	0.00e+00	0.392	0.182	Malignant cells	NA
PYCARD	ENSG00000103490	0.340942	0.00e+00	6.99e-43	0.685	0.551	Malignant cells	NA
OLFM1	ENSG00000130558	0.3406	0.00e+00	0.00e+00	0.253	0.046	Malignant cells	NA
TWF2	ENSG00000247596	0.340091	0.00e+00	0.00e+00	0.652	0.493	Malignant cells	NA
PTRH1	ENSG00000187024	0.339851	0.00e+00	0.00e+00	0.632	0.469	Malignant cells	NA
SH3PXD2A	ENSG00000107957	0.339695	0.00e+00	0.00e+00	0.265	0.049	Malignant cells	NA
MRPL45	ENSG00000277936	0.339263	0.00e+00	0.00e+00	0.523	0.335	Malignant cells	NA
CCT3	ENSG00000163468	0.339241	0.00e+00	0.00e+00	0.899	0.801	Malignant cells	NA
VAMP2	ENSG00000220205	0.339076	0.00e+00	0.00e+00	0.794	0.69	Malignant cells	NA
C19orf70	NA	0.338615	0.00e+00	0.00e+00	0.951	0.928	Malignant cells	NA
NAT9	ENSG00000109065	0.33762	0.00e+00	0.00e+00	0.508	0.335	Malignant cells	NA
GHITM	ENSG00000165678	0.337117	0.00e+00	0.00e+00	0.932	0.89	Malignant cells	NA
HADHA	ENSG00000084754	0.337063	0.00e+00	0.00e+00	0.701	0.556	Malignant cells	NA
INO80B	ENSG00000115274	0.336732	0.00e+00	0.00e+00	0.523	0.346	Malignant cells	NA
SAV1	ENSG00000151748	0.335399	6.68e-40	1.21e-35	0.694	0.583	Malignant cells	NA
IER5L	ENSG00000188483	0.335093	0.00e+00	0.00e+00	0.349	0.159	Malignant cells	NA
C10orf118	NA	0.334988	0.00e+00	0.00e+00	0.437	0.229	Malignant cells	NA
IBTK	ENSG00000283068	0.334321	0.00e+00	0.00e+00	0.389	0.195	Malignant cells	NA
PRKAR1A	ENSG00000108946	0.334127	0.00e+00	0.00e+00	0.682	0.534	Malignant cells	NA
PTP4A3	ENSG00000275575	0.333874	0.00e+00	0.00e+00	0.265	0.057	Malignant cells	NA
SDSL	ENSG00000139410	0.333623	0.00e+00	0.00e+00	0.363	0.143	Malignant cells	NA
NKD2	ENSG00000276920	0.33322	0.00e+00	0.00e+00	0.363	0.166	Malignant cells	NA
PGM3	ENSG00000013375	0.33277	0.00e+00	0.00e+00	0.319	0.107	Malignant cells	NA
RARS2	ENSG00000146282	0.332769	0.00e+00	0.00e+00	0.521	0.344	Malignant cells	NA
IRF7	ENSG00000276561	0.332555	0.00e+00	0.00e+00	0.434	0.252	Malignant cells	NA
PPP1R7	ENSG00000115685	0.33206	0.00e+00	0.00e+00	0.569	0.405	Malignant cells	NA
MARK3	ENSG00000075413	0.331457	0.00e+00	0.00e+00	0.647	0.495	Malignant cells	NA
SMAD3	ENSG00000166949	0.331009	0.00e+00	6.61e-43	0.747	0.649	Malignant cells	NA
STK39	ENSG00000198648	0.330961	0.00e+00	0.00e+00	0.286	0.074	Malignant cells	NA
PHGDH	ENSG00000092621	0.330584	0.00e+00	0.00e+00	0.483	0.311	Malignant cells	NA
RHOF	ENSG00000139725	0.330255	2.38e-44	4.24e-40	0.88	0.857	Malignant cells	NA
ARFGAP3	ENSG00000242247	0.330138	0.00e+00	0.00e+00	0.4	0.194	Malignant cells	NA
DNASE2	ENSG00000105612	0.329755	0.00e+00	0.00e+00	0.367	0.164	Malignant cells	NA
HES1	ENSG00000114315	0.328835	4.89e-38	8.87e-34	0.799	0.723	Malignant cells	NA
PFKL	ENSG00000141959	0.328762	0.00e+00	0.00e+00	0.558	0.376	Malignant cells	NA
ARHGAP18	ENSG00000146376	0.3287	0.00e+00	0.00e+00	0.306	0.101	Malignant cells	NA
SLC35D2	ENSG00000130958	0.327375	0.00e+00	0.00e+00	0.448	0.265	Malignant cells	NA
ARHGAP26	ENSG00000145819	0.326901	0.00e+00	0.00e+00	0.34	0.131	Malignant cells	NA
ACADVL	ENSG00000072778	0.32688	0.00e+00	0.00e+00	0.794	0.701	Malignant cells	NA
XPNPEP1	ENSG00000108039	0.32514	0.00e+00	0.00e+00	0.378	0.171	Malignant cells	NA
NT5C2	ENSG00000076685	0.324706	0.00e+00	2.80e-45	0.52	0.358	Malignant cells	NA
TUBE1	ENSG00000074935	0.323984	0.00e+00	0.00e+00	0.344	0.136	Malignant cells	NA
FKBP8	ENSG00000105701	0.323688	0.00e+00	0.00e+00	0.96	0.932	Malignant cells	NA
CCNC	ENSG00000112237	0.323582	3.22e-44	5.92e-40	0.722	0.632	Malignant cells	NA
PNPLA2	ENSG00000177666	0.323084	0.00e+00	0.00e+00	0.511	0.335	Malignant cells	NA
MMADHC	ENSG00000168288	0.323079	0.00e+00	0.00e+00	0.834	0.746	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	5.00e-21	2.50e-20	3441	781	214	23467	Malignant cells	AKT2,ATG12,AURKA,BAX,BBC3,BIK,BIRC5,BRCA1,CDK4,CDK6,CDKN1A,CERS2,DCTD,DNMT1,DUSP6,EGFR,FUBP1,GLS,GSTP1,SLC2A1,HMGA1,HMGB1,ID1,EIF4G1,ISG15,JUN,PKM,MCL1,MAPK1,MAP1LC3B,MTA1,NFE2L2,NFKB1,PARP1,PEA15,PPARG,PTEN,RAB6A,KRAS,RALBP1,RHOA,RPS6,S100A4,SOCS2,SOX2,STMN1,TGFBR2,PBK,TPD52,TRIM16,TYMS,VEGFA,VOPP1,XIAP,YAP1,YWHAZ,NT5C2,AAMDC,SLC25A5,AGR2,AKAP12,AKT3,ANXA1,TFAP2A,BAD,BAG3,BID,HSPA5,BRD4,BRD7,BTG1,CAV2,CCNA2,CCNB1,CDK1,CCND1,CCNE1,ALCAM,CDC27,CDK2,HSPD1,CSF1,CTNND1,CUL4A,DCK,DDIT3,DKK1,DHFR,E2F1,E2F3,EHF,HSP90B1,EPHA2,ERRFI1,EZH2,EZR,FAT1,FGFR1,FN1,FIS1,FOXM1,FTL,FUS,GAS6,NR3C1,GRB2,GCLM,GCLC,GSR,SLC16A3,HDAC3,HIPK2,HMGB2,HSPB1,HK1,IDH1,EIF4E,EIF5A2,JAG1,KEAP1,KLF4,LAMP3,LASP1,LDHA,LRRFIP1,MTDH,NF2,MAPK3,MOB1A,MAP2K1,MYBL2,MYD88,MYO10,NDST1,NFYB,NKD2,NUCKS1,OAZ2,SPP1,PDE4D,PGK1,PLK1,POMP,PRKDC,RAC1,RAF1,RANGAP1,RAP1A,RAP1B,HRAS,NRAS,RAB27A,RECK,RNF2,RRM1,RRM2,HNRNPA1,RUNX2,SAV1,SDHB,SFPQ,SMAD3,SMC4,SNAI2,SOD2,SRI,SPIN1,SRSF2,STARD10,RBPJ,TFAM,TMED3,TMEM54,TNFAIP3,TOP1,UBE2C,USP22,AXL,P
Drug Inactivation by Structure Modification	3.50e-02	8.80e-02	3441	27	8	23467	Malignant cells	GSTP1,NT5C2,CYP1B1,DCK,CES1,SOD2,CDA,NME1
Aberration of the Drug's Therapeutic Target	4.50e-01	5.80e-01	3441	90	14	23467	Malignant cells	AKT2,BRCA1,CDK4,CDK6,EGFR,DHFR,EZH2,FGFR1,IDH1,MAP2K1,JAK1,NPM1,AKR1B1,TOP2A
Irregularity in Drug Uptake and Drug Efflux	4.60e-01	5.80e-01	3441	37	6	23467	Malignant cells	SLC3A2,SLC2A1,ABCC1,ABCF2,SLC7A5,ABCC5
Epigenetic Alteration of DNA, RNA or Protein	1.00e+00	1.00e+00	3441	455	25	23467	Malignant cells	BIK,DNMT1,EGFR,H2AFY,EIF4G2,LMNA,MTA1,PPARG,TRIP6,TYMS,XIAP,BMF,EZH2,IDH1,MAPK3,SMC4,TIMP1,MALAT1,GDI2,AKT3,PPP1R15A,SMYD2,MT-CO2,DLEU1,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
	taipale_tf_pairs__ATF4_TEF_RNMTGATGCAATN_CAP	4.96	0.0538	ATF4; TEF (directAnnotation).	Malignant cells
	taipale_tf_pairs__ELK1_TEF_NSCGGAWNTTACGTAAN_CAP	4.8	0.053	ELK1; TEF (directAnnotation).	Malignant cells
	taipale_tf_pairs__ATF4_CEBPD_NGATGATGCAATNN_CAP	4.6	0.052	ATF4; CEBPD (directAnnotation).	Malignant cells
	jaspar__MA1933.1	3.96	0.0487	SREBF2 (directAnnotation).	Malignant cells
	metacluster_174.3	3.72	0.0476	MBD2; NFYA; NFYB; NFYC; PBX3 (directAnnotation).	Malignant cells
	transfac_pro__M01299	3.68	0.0473	MECP2 (directAnnotation).	Malignant cells
	metacluster_156.2	3.62	0.0471	ATF3; ATF4; ATF4; ATF4; ATF4; ATF4; ATF4; CEBPG; CEBPG; DDIT3; MYC (directAnnotation). ATF4; ATF4; ATF4; CEBPG; DDIT3 (inferredBy_Orthology).	Malignant cells
	transfac_pro__M06213	3.55	0.0467	ZNF267 (directAnnotation).	Malignant cells
	transfac_pro__M06035	3.45	0.0462	ZNF749 (directAnnotation).	Malignant cells
	transfac_pro__M01861	3.44	0.0462	ATF1 (directAnnotation).	Malignant cells

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Motifs and TFs regulating down-regulated DEGs in resistant group

motif	motif	NES	AUC	TF_highConf	Cell_type
	metacluster_174.3	4.61	0.0472	MBD2; NFYA; NFYB; NFYC; PBX3 (directAnnotation).	Malignant cells
	metacluster_174.2	4.55	0.0469	CEBPZ; CEBPZ; DRAP1; FOS; FOXI1; FOXI1; HMGXB3; IRF3; NFYA; NFYA; NFYA; NFYA; NFYA; NFYA; NFYA; NFYA; NFYA; NFYB; NFYB; NFYB; NFYB; NFYB; NFYC; NFYC; NFYC; NFYC; NFYC; NFYC; NFYC; PBX3; PBX3; SP2 (directAnnotation). NFYA; NFYA; NFYC; PBX1; PBX3 (inferredBy_Orthology).	Malignant cells
	metacluster_191.2	4.23	0.0455	ELK4; NR2C2; NR2C2; NR2C2; NR2C2 (directAnnotation). GABPA (inferredBy_Orthology).	Malignant cells
	metacluster_55.3	4.11	0.0449	E2F6; EGR1; NRF1; NRF1; NRF1; NRF1; NRF1; NRF1; NRF1; NRF1; NRF1; NRF1; ZBTB2; ZSCAN10 (directAnnotation). NFE2L1; NRF1; NRF1; NRF1 (inferredBy_Orthology).	Malignant cells
	taipale_tf_pairs__ETS2_RCCGGAAGTG_HT	4.09	0.0449	ETS2 (directAnnotation).	Malignant cells
	dbtfbs__E2F8_representative_N1	4.08	0.0448	E2F8 (directAnnotation).	Malignant cells
	jaspar__MA1483.2	3.97	0.0443	ELF2 (directAnnotation).	Malignant cells
	transfac_pro__M04950	3.97	0.0443	EGR1 (directAnnotation).	Malignant cells
	metacluster_34.4	3.96	0.0443	ETS1; ETS1; ETS1; HCFC1; SIX5; SIX5; SIX5; SIX5; SMARCC2; SMARCC2; THAP11; THAP11; ZNF143; ZNF143; ZNF143; ZNF143 (directAnnotation). TBX2; THAP11; THAP11; ZNF143 (inferredBy_Orthology).	Malignant cells
	metacluster_15.3	3.89	0.0439	E2F1; E2F6; E2F8; E2F8; TFDP1 (directAnnotation). E2F3 (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
EHF	metacluster_191.3	up	Malignant cells	NA
ETV5	metacluster_191.3	up	Malignant cells	NA
SPDEF	metacluster_191.3	up	Malignant cells	NA
ETV5	taipale_tf_pairs__ETV5_HOXA2_RSCGGWAATKR_CAP	up	Malignant cells	NA
HDAC2	transfac_pro__M04866	up	Malignant cells	NA
EHF	metacluster_166.4	up	Malignant cells	NA
ETV5	metacluster_166.4	up	Malignant cells	NA
ELF3	metacluster_166.4	up	Malignant cells	NA
ETV5	metacluster_138.2	up	Malignant cells	NA
SPDEF	metacluster_138.2	up	Malignant cells	NA

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