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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
	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: GSE164551

Dataset summary for GSE164551

Datast information	Dataset	GSE164551
	PMID	33558511
	Raw data ID/link	https://doi.org/10.7910/DVN/1RKYQ8
	Organism	Homo sapiens
	Source	patients
	Tissue	Bone marrow aspirate
	Cancer type level1	Multiple myeloma
	Cancer type level2	Refractory multiple myeloma (MM)
	Regimen	CAR-T
	Drug type	Immunotherapy
	Sample size	resistant 1, sensitive 1
	Cell number	7736
	Extract protocol	10x genomics
	Data processing	CellRanger 3.1.0
	Public date	Public on Jan 11, 2021
	Description	This dataset has 1 patient with a sensitive pre-treatment sample and a resistant post-treatment sample.

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Drug summary for GSE164551

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"CAR-T" is not included in the drug list.

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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

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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.)

resistant vs. sensitive

Dot plot of significant ligand-receptor pairs in the resistant group	Dot plot of significant ligand-receptor pairs in the sensitive group

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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
DDX3X	ENSG00000215301	-0.256884	1.38e-11	2.17e-07	0.243	0.409	Erythrocytes	NA
ARF1	ENSG00000143761	-0.257144	8.77e-14	1.38e-09	0.225	0.403	Erythrocytes	NA
YPEL5	ENSG00000119801	-0.25907	2.30e-09	3.62e-05	0.168	0.295	Erythrocytes	NA
UQCR11	ENSG00000127540	-0.260113	1.10e-10	1.74e-06	0.237	0.383	Erythrocytes	NA
PTMS	ENSG00000159335	-0.260258	1.95e-11	3.07e-07	0.157	0.301	Erythrocytes	NA
PHIP	ENSG00000146247	-0.260414	1.74e-12	2.74e-08	0.167	0.327	Erythrocytes	NA
EHBP1L1	ENSG00000173442	-0.262272	2.02e-11	3.18e-07	0.132	0.269	Erythrocytes	NA
MZT2B	ENSG00000152082	-0.262792	4.59e-10	7.24e-06	0.188	0.321	Erythrocytes	NA
ITM2B	ENSG00000136156	-0.263566	2.35e-12	3.71e-08	0.369	0.537	Erythrocytes	NA
DDX6	ENSG00000110367	-0.263682	6.36e-12	1.00e-07	0.247	0.415	Erythrocytes	NA
PPDPF	ENSG00000125534	-0.264687	3.88e-13	6.12e-09	0.162	0.323	Erythrocytes	NA
EWSR1	ENSG00000182944	-0.265006	2.12e-16	3.35e-12	0.105	0.277	Erythrocytes	NA
ATG3	ENSG00000144848	-0.26512	1.07e-15	1.69e-11	0.1	0.262	Erythrocytes	NA
AMMECR1	ENSG00000101935	-0.265251	2.46e-14	3.88e-10	0.144	0.311	Erythrocytes	NA
AC100835.2	NA	-0.265847	1.17e-12	1.85e-08	0.33	0.511	Erythrocytes	NA
CD44	ENSG00000026508	-0.266739	9.19e-11	1.45e-06	0.201	0.349	Erythrocytes	NA
PAPOLA	ENSG00000090060	-0.268542	1.46e-14	2.30e-10	0.118	0.275	Erythrocytes	NA
CTSL	ENSG00000135047	-0.270399	8.28e-11	1.31e-06	0.188	0.337	Erythrocytes	NA
CSDE1	ENSG00000009307	-0.270954	1.13e-13	1.79e-09	0.209	0.38	Erythrocytes	NA
PSAP	ENSG00000197746	-0.271012	2.34e-11	3.69e-07	0.165	0.309	Erythrocytes	NA
TMEM59	ENSG00000116209	-0.272362	2.24e-11	3.52e-07	0.292	0.44	Erythrocytes	NA
CAPZA2	ENSG00000198898	-0.272441	1.36e-16	2.14e-12	0.105	0.277	Erythrocytes	NA
SNX3	ENSG00000112335	-0.274505	7.45e-09	1.17e-04	0.541	0.636	Erythrocytes	NA
ALAD	ENSG00000148218	-0.276362	1.27e-13	2.00e-09	0.137	0.293	Erythrocytes	NA
PRKAR2B	ENSG00000284096	-0.278791	2.75e-15	4.33e-11	0.121	0.287	Erythrocytes	NA
SPECC1	ENSG00000128487	-0.279441	1.42e-11	2.23e-07	0.243	0.398	Erythrocytes	NA
ODC1	ENSG00000115758	-0.279697	1.44e-12	2.27e-08	0.194	0.351	Erythrocytes	NA
EID1	ENSG00000255302	-0.280441	9.67e-19	1.52e-14	0.078	0.253	Erythrocytes	NA
ZNF207	ENSG00000010244	-0.28093	8.68e-15	1.37e-10	0.139	0.308	Erythrocytes	NA
PRDX6	ENSG00000117592	-0.282087	9.05e-11	1.43e-06	0.508	0.641	Erythrocytes	NA
SNW1	ENSG00000100603	-0.282492	4.83e-20	7.61e-16	0.08	0.262	Erythrocytes	NA
EMC3	ENSG00000125037	-0.282927	2.27e-07	3.57e-03	0.373	0.478	Erythrocytes	NA
UBA52	ENSG00000221983	-0.283143	1.43e-08	2.26e-04	0.895	0.872	Erythrocytes	NA
PPIG	ENSG00000138398	-0.28401	1.10e-16	1.73e-12	0.095	0.266	Erythrocytes	NA
DHX9	ENSG00000135829	-0.284442	1.15e-15	1.82e-11	0.101	0.262	Erythrocytes	NA
EIF3B	ENSG00000106263	-0.284818	4.08e-16	6.43e-12	0.096	0.262	Erythrocytes	NA
NEDD8	ENSG00000285246	-0.285828	8.39e-20	1.32e-15	0.074	0.251	Erythrocytes	NA
MYL12B	ENSG00000118680	-0.286786	4.57e-16	7.20e-12	0.19	0.376	Erythrocytes	NA
REXO2	ENSG00000076043	-0.287442	1.31e-08	2.07e-04	0.25	0.372	Erythrocytes	NA
ILF3	ENSG00000129351	-0.287732	7.14e-15	1.13e-10	0.098	0.25	Erythrocytes	NA
RAD23A	ENSG00000179262	-0.287785	7.26e-12	1.15e-07	0.56	0.697	Erythrocytes	NA
NDFIP1	ENSG00000131507	-0.287821	2.20e-16	3.47e-12	0.137	0.316	Erythrocytes	NA
PRPF40A	ENSG00000196504	-0.288305	8.31e-20	1.31e-15	0.077	0.26	Erythrocytes	NA
TUBB2A	ENSG00000137267	-0.288431	1.59e-06	2.51e-02	0.513	0.584	Erythrocytes	NA
MBNL1	ENSG00000152601	-0.289243	5.87e-16	9.26e-12	0.173	0.356	Erythrocytes	NA
C11orf58	ENSG00000110696	-0.292887	1.65e-18	2.60e-14	0.093	0.27	Erythrocytes	NA
HSPA5	ENSG00000044574	-0.294221	2.69e-11	4.24e-07	0.186	0.335	Erythrocytes	NA
SLC7A5	ENSG00000103257	-0.295976	3.20e-11	5.04e-07	0.288	0.445	Erythrocytes	NA
EIF3K	ENSG00000282986	-0.296039	4.22e-14	6.66e-10	0.127	0.282	Erythrocytes	NA
PLIN2	ENSG00000147872	-0.296631	3.28e-16	5.18e-12	0.092	0.253	Erythrocytes	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	5.90e-02	2.90e-01	12	781	2	23467	Malignant cells	EGR1,CXCL8
Epigenetic Alteration of DNA, RNA or Protein	2.10e-01	5.20e-01	12	455	1	23467	Malignant cells	CXCL8
Aberration of the Drug's Therapeutic Target	1.00e+00	1.00e+00	12	90	0	23467	Malignant cells
Drug Inactivation by Structure Modification	1.00e+00	1.00e+00	12	27	0	23467	Malignant cells
Irregularity in Drug Uptake and Drug Efflux	1.00e+00	1.00e+00	12	37	0	23467	Malignant cells

Enrichment results for 1 known drug resistance mechanisms in TME cells

Mechnism	Pval	FDR	Signature	Geneset	Overlap	Background	Cell type	Enriched Genes
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	3	186	0	23467	B cells	NA
Regulation by the Disease Microenvironment	6.60e-03	6.60e-03	148	186	5	23467	CD4+ T cells	BRAF,TGFB1,SOCS3,VIM,ZEB1
Regulation by the Disease Microenvironment	1.80e-01	1.80e-01	276	186	4	23467	CD8+ T cells	NFKB1,TGFB1,CXCR4,VIM
Regulation by the Disease Microenvironment	5.10e-01	5.10e-01	467	186	4	23467	Erythrocytes	BCL2L1,MTDH,HNRNPA2B1,MALAT1
Regulation by the Disease Microenvironment	9.20e-03	9.20e-03	524	186	10	23467	Mono_Macro	BRAF,CTNNB1,TGFB1,VEGFA,ZEB2,IL1B,HNRNPA2B1,SOCS3,VIM,MALAT1
Regulation by the Disease Microenvironment	4.80e-01	4.80e-01	81	186	1	23467	NK cells	VIM

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
This dataset does not contain malignant cells, nor does it predict any miRNA that corresponds to the top10 DEGs.

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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__M02848	4.05	0.193	EGR1 (inferredBy_Orthology).	CD4+ T cells
	taipale_tf_pairs__ETV5_HES7_NNCACGTGNNNNCCGGAANN_CAP	4.02	0.192	ETV5; HES7 (directAnnotation).	CD4+ T cells
	transfac_pro__M07475	3.81	0.185	TBX5 (inferredBy_Orthology).	CD4+ T cells
	cisbp__M00775	3.79	0.184	ZBTB1 (inferredBy_Orthology).	CD4+ T cells
	metacluster_84.2	3.76	0.183	RARA (directAnnotation).	CD4+ T cells
	taipale_tf_pairs__E2F1_ELK1_SGCGCNNNNNNNNNNCGGAAGN_CAP_repr	3.74	0.182	E2F1; ELK1 (directAnnotation).	CD4+ T cells
	metacluster_141.5	3.71	0.181	NR3C1; THAP1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY2; YY2; ZNF597 (directAnnotation). YY1; YY1; YY1; YY2; ZFP42 (inferredBy_Orthology).	CD4+ T cells
	jaspar__MA1650.1	3.68	0.18	ZBTB14 (directAnnotation).	CD4+ T cells
	transfac_pro__M02090	3.62	0.178	E2F4 (directAnnotation).	CD4+ T cells
	transfac_pro__M08005	3.56	0.176	TCFL5 (inferredBy_Orthology).	CD4+ T cells

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Motifs and TFs regulating down-regulated DEGs in resistant group

motif	motif	NES	AUC	TF_highConf	Cell_type
	transfac_pro__M01252	7.71	0.61	E2F6 (directAnnotation).	B cells
	tfdimers__MD00310	7.02	0.558	IKZF1; OTX1; OTX2 (directAnnotation).	B cells
	metacluster_76.1	6.65	0.53	ZNF345; ZNF345 (directAnnotation). MYB; MYBL1 (inferredBy_Orthology).	B cells
	metacluster_156.2	6.56	0.523	ATF3; ATF4; ATF4; ATF4; ATF4; ATF4; ATF4; CEBPG; CEBPG; DDIT3; MYC (directAnnotation). ATF4; ATF4; ATF4; CEBPG; DDIT3 (inferredBy_Orthology).	B cells
	transfac_pro__M05531	6.5	0.518	IKZF5 (inferredBy_Orthology).	B cells
	tfdimers__MD00103	6.44	0.514	ZNF333 (directAnnotation).	B cells
	cisbp__M00838	6.02	0.482	FOXP1 (directAnnotation).	B cells
	metacluster_130.1	5.99	0.48	ZNF713; ZNF713 (directAnnotation). HSF1; HSF2; HSF4; HSF5; HSFX1; HSFX2; HSFX3; HSFX4; HSFY1; HSFY2 (inferredBy_Orthology).	B cells
	metacluster_139.9	5.89	0.473	TFE3 (inferredBy_Orthology).	B cells
	tfdimers__MD00298	5.88	0.471	CEBPA; CEBPB; CEBPD; CEBPE; CEBPG; FOXL1 (directAnnotation).	B 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
ZEB1	tfdimers__MD00527	up	CD4+ T cells	NA
MECP2	metacluster_135.10	up	CD8+ T cells	NA
E2F4	metacluster_45.6	down	Erythrocytes	NA
KLF13	hocomoco__KLF13_HUMAN.H11MO.0.D	down	Erythrocytes	NA
YBX1	metacluster_79.33	down	Erythrocytes	NA
BACH1	metacluster_22.37	up	Mono/Macro	NA
BACH1	metacluster_157.2	up	Mono/Macro	NA
BACH1	metacluster_30.4	up	Mono/Macro	NA
EGR1	cisbp__M01864	up	Mono/Macro	NA
EGR1	metacluster_131.7	up	Mono/Macro	NA

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