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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
	Comparison of intra-tumor heterogeneity (ITH) and epithelial-mesenchymal transition (EMT) scores of malignant cells between the resistant and sensitive groups (This dataset does not contain this module)
	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
	Mechanism analysis of drug resistance-related DEGs for each cell type in the post-treatment samples
	Mechanism analysis of drug resistance-related DEGs for each cell type in one patient or cell lines (This dataset does not contain this module)
	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: GSE212217

Dataset summary for GSE212217

Datast information	Dataset	GSE212217
	PMID	36301137
	Raw data ID/link	PRJNA874603
	Organism	Homo sapiens
	Source	patients
	Tissue	Peripheral blood mononuclear cells
	Cancer type level1	Endometrial cancer
	Cancer type level2	Epigenetic MMRd endometrial carcinoma
	Regimen	pembrolizumab
	Drug type	Immunotherapy
	Sample size	pre (resistant 9, sensitive 12); post (resistant 9, sensitive 12)
	Cell number	224785
	Extract protocol	10x genomics
	Data processing	CellRanger
	Public date	Public on Oct 07, 2022
	Description	This dataset has 22 patients, 20 of whom has both pre- and post-treatment samples.

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Drug summary for GSE212217

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"Pembrolizumab"	DB09037	biotech	PDCD1; CD274	Q15116; Q9NZQ7

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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.)

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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.)

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

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.)

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

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.

Gene symbol	Gene id	avg_log2FC	p_val	p_val_adj	pct.1	pct.2	Cell type	Timepoint
LILRB4	ENSG00000278555	0.553658	4.56e-08	9.76e-04	0.436	0.185	Plasma cells	pre
CRELD2	ENSG00000184164	0.424491	1.07e-06	2.29e-02	0.8	0.645	Plasma cells	pre
GAS6	ENSG00000183087	0.401592	1.04e-06	2.22e-02	0.394	0.175	Plasma cells	pre
TSPO	ENSG00000100300	-0.453376	2.86e-07	6.13e-03	0.139	0.365	Plasma cells	pre
RPS26	ENSG00000197728	-0.738349	1.15e-12	2.45e-08	0.879	0.95	Plasma cells	pre
SNHG5	ENSG00000203875	-0.44926	1.22e-11	2.61e-07	0.335	0.604	pDCs	pre
RPL21	ENSG00000122026	-0.469806	1.76e-08	3.76e-04	0.932	0.938	pDCs	pre
MTRNR2L12	NA	-0.574654	1.74e-06	3.73e-02	0.912	0.956	pDCs	pre
RPS26	ENSG00000197728	-0.705726	6.40e-22	1.37e-17	0.94	0.993	pDCs	pre
CD3E	ENSG00000198851	0.698261	0.00e+00	0.00e+00	0.682	0.455	NK cells	pre
MYOM2	ENSG00000274137	0.616259	0.00e+00	0.00e+00	0.44	0.198	NK cells	pre
MT-ND4	ENSG00000198886	0.429007	0.00e+00	0.00e+00	0.994	0.992	NK cells	pre
DUSP1	ENSG00000120129	0.373158	8.67e-43	1.86e-38	0.653	0.56	NK cells	pre
ZFP36	ENSG00000128016	0.352662	1.33e-32	2.85e-28	0.737	0.69	NK cells	pre
FOS	ENSG00000170345	0.336638	4.67e-14	1.00e-09	0.432	0.379	NK cells	pre
ZFP36L2	ENSG00000152518	0.27587	0.00e+00	0.00e+00	0.914	0.873	NK cells	pre
RPS14	ENSG00000164587	0.259546	0.00e+00	0.00e+00	1	1	NK cells	pre
RPS28	ENSG00000233927	0.259136	0.00e+00	0.00e+00	1	1	NK cells	pre
CD74	ENSG00000019582	-0.252987	9.32e-33	1.99e-28	0.904	0.917	NK cells	pre
HLA-A	ENSG00000227715	-0.265163	0.00e+00	0.00e+00	1	1	NK cells	pre
RPL21	ENSG00000122026	-0.273284	0.00e+00	0.00e+00	0.966	0.96	NK cells	pre
IFITM1	ENSG00000185885	-0.305606	0.00e+00	0.00e+00	0.998	0.999	NK cells	pre
MT-ATP8	ENSG00000228253	-0.321421	1.48e-30	3.16e-26	0.938	0.949	NK cells	pre
KIR3DL1	ENSG00000276379	-0.342202	0.00e+00	0.00e+00	0.12	0.262	NK cells	pre
MTRNR2L12	NA	-0.345433	0.00e+00	0.00e+00	0.968	0.98	NK cells	pre
RPS26	ENSG00000197728	-0.47564	0.00e+00	0.00e+00	0.98	0.993	NK cells	pre
IFITM3	ENSG00000142089	-0.563495	0.00e+00	0.00e+00	0.578	0.718	NK cells	pre
TMEM176A	ENSG00000002933	0.430208	0.00e+00	0.00e+00	0.419	0.206	Mono/Macro	pre
CEBPD	ENSG00000221869	0.382394	0.00e+00	0.00e+00	0.882	0.765	Mono/Macro	pre
TMEM176B	ENSG00000106565	0.355735	0.00e+00	0.00e+00	0.507	0.307	Mono/Macro	pre
MT2A	ENSG00000125148	0.325577	3.05e-41	6.53e-37	0.657	0.558	Mono/Macro	pre
NFKBIA	ENSG00000100906	0.322901	4.62e-44	1.00e-39	0.786	0.715	Mono/Macro	pre
VIM	ENSG00000026025	0.317325	0.00e+00	0.00e+00	0.997	0.994	Mono/Macro	pre
VCAN	ENSG00000038427	0.307443	0.00e+00	0.00e+00	0.789	0.683	Mono/Macro	pre
MCL1	ENSG00000143384	0.305824	0.00e+00	0.00e+00	0.802	0.719	Mono/Macro	pre
SERPINB1	ENSG00000021355	0.30558	0.00e+00	0.00e+00	0.661	0.54	Mono/Macro	pre
GAPDH	ENSG00000111640	0.303092	0.00e+00	0.00e+00	0.998	0.996	Mono/Macro	pre
PLBD1	ENSG00000121316	0.265487	0.00e+00	0.00e+00	0.471	0.355	Mono/Macro	pre
FOS	ENSG00000170345	0.263601	0.00e+00	1.26e-43	0.96	0.94	Mono/Macro	pre
LGALS2	ENSG00000100079	0.251357	0.00e+00	0.00e+00	0.632	0.397	Mono/Macro	pre
TXNIP	ENSG00000265972	-0.250223	0.00e+00	0.00e+00	0.849	0.914	Mono/Macro	pre
SNHG5	ENSG00000203875	-0.288152	0.00e+00	0.00e+00	0.291	0.423	Mono/Macro	pre
HMOX1	ENSG00000100292	-0.288158	3.81e-23	8.15e-19	0.412	0.47	Mono/Macro	pre
LYZ	ENSG00000090382	-0.294432	0.00e+00	2.00e-42	0.961	0.975	Mono/Macro	pre
MT-ND3	ENSG00000198840	-0.300043	0.00e+00	0.00e+00	1	1	Mono/Macro	pre
MS4A7	ENSG00000166927	-0.311514	9.01e-29	1.93e-24	0.499	0.562	Mono/Macro	pre
LST1	ENSG00000235915	-0.356628	9.82e-40	2.10e-35	0.927	0.927	Mono/Macro	pre
AC253572.2	NA	-0.421019	2.94e-44	6.26e-40	0.219	0.31	Mono/Macro	pre
MTRNR2L12	NA	-0.42782	0.00e+00	0.00e+00	0.916	0.964	Mono/Macro	pre
RPL21	ENSG00000122026	-0.476216	0.00e+00	0.00e+00	0.88	0.931	Mono/Macro	pre

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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.

Gene symbol	Gene id	avg_log2FC	p_val	p_val_adj	pct.1	pct.2	Cell type	Timepoint
MYDGF	ENSG00000074842	0.618441	5.37e-09	1.15e-04	0.95	0.916	Plasma cells	post
MZB1	ENSG00000170476	0.592471	1.48e-11	3.17e-07	0.995	0.995	Plasma cells	post
MT-ND2	ENSG00000198763	0.545552	5.96e-10	1.28e-05	0.89	0.747	Plasma cells	post
HSP90B1	ENSG00000166598	0.536456	1.12e-07	2.40e-03	0.995	1	Plasma cells	post
HLA-C	ENSG00000206435	0.532811	3.24e-08	6.93e-04	0.985	0.968	Plasma cells	post
SEC11C	ENSG00000166562	0.484688	2.86e-08	6.11e-04	0.98	0.958	Plasma cells	post
MT-ND3	ENSG00000198840	0.467335	8.15e-10	1.74e-05	1	0.979	Plasma cells	post
FNDC3B	ENSG00000075420	0.45281	2.19e-08	4.68e-04	0.59	0.326	Plasma cells	post
FKBP11	ENSG00000134285	0.448331	7.19e-09	1.54e-04	0.93	0.905	Plasma cells	post
SPCS3	ENSG00000129128	0.446694	4.93e-10	1.06e-05	0.925	0.916	Plasma cells	post
LMAN1	ENSG00000074695	0.435891	5.02e-08	1.07e-03	0.925	0.879	Plasma cells	post
PRDX4	ENSG00000123131	0.434841	1.87e-06	3.99e-02	0.805	0.7	Plasma cells	post
P4HB	ENSG00000185624	0.43464	5.57e-07	1.19e-02	0.94	0.937	Plasma cells	post
IFI30	ENSG00000216490	0.409574	1.11e-07	2.36e-03	0.65	0.411	Plasma cells	post
GAS6	ENSG00000183087	0.383617	4.37e-08	9.36e-04	0.355	0.121	Plasma cells	post
GGH	ENSG00000137563	0.361336	7.37e-07	1.58e-02	0.465	0.232	Plasma cells	post
AC012236.1	NA	0.35296	1.15e-06	2.46e-02	0.43	0.211	Plasma cells	post
FCRL5	ENSG00000143297	0.333276	8.26e-07	1.77e-02	0.435	0.211	Plasma cells	post
CPEB4	ENSG00000113742	0.3222	4.91e-07	1.05e-02	0.305	0.1	Plasma cells	post
SNHG5	ENSG00000203875	-0.33802	1.83e-07	3.92e-03	0.16	0.395	Plasma cells	post
RPL10	ENSG00000147403	-0.344037	4.58e-07	9.80e-03	0.99	1	Plasma cells	post
EEF1A1	ENSG00000156508	-0.344909	1.93e-06	4.13e-02	0.995	0.989	Plasma cells	post
PTPN6	ENSG00000111679	-0.361926	9.69e-07	2.07e-02	0.195	0.416	Plasma cells	post
CD79A	ENSG00000105369	-0.439624	8.29e-08	1.77e-03	0.765	0.947	Plasma cells	post
RPS15A	ENSG00000134419	-0.471403	2.82e-09	6.03e-05	0.99	0.989	Plasma cells	post
RPS26	ENSG00000197728	-0.47229	2.89e-08	6.17e-04	0.915	0.968	Plasma cells	post
CD52	ENSG00000169442	-0.475887	5.30e-09	1.13e-04	0.41	0.726	Plasma cells	post
ARHGDIB	ENSG00000111348	-0.498886	8.51e-08	1.82e-03	0.455	0.726	Plasma cells	post
S100A6	ENSG00000197956	-0.507625	3.18e-08	6.80e-04	0.355	0.668	Plasma cells	post
TSPO	ENSG00000100300	-0.512689	4.43e-10	9.48e-06	0.155	0.437	Plasma cells	post
S100A4	ENSG00000196154	-0.766314	1.70e-07	3.64e-03	0.215	0.447	Plasma cells	post
MT-ATP8	ENSG00000228253	0.466267	5.06e-12	1.08e-07	0.92	0.753	pDCs	post
RPS29	ENSG00000213741	0.346743	1.77e-11	3.79e-07	0.989	0.959	pDCs	post
MT-ND3	ENSG00000198840	0.325043	6.62e-07	1.42e-02	1	0.993	pDCs	post
RPL38	ENSG00000172809	0.273482	2.02e-06	4.31e-02	0.954	0.894	pDCs	post
RPS26	ENSG00000197728	-1.13971	0.00e+00	3.64e-44	0.924	0.995	pDCs	post
CD3E	ENSG00000198851	0.522902	0.00e+00	0.00e+00	0.624	0.443	NK cells	post
MYOM2	ENSG00000274137	0.339123	0.00e+00	0.00e+00	0.374	0.244	NK cells	post
TGFB1	ENSG00000105329	0.287839	0.00e+00	0.00e+00	0.736	0.632	NK cells	post
MT-ND3	ENSG00000198840	0.270148	0.00e+00	0.00e+00	1	0.999	NK cells	post
MT-ATP8	ENSG00000228253	0.267287	0.00e+00	0.00e+00	0.976	0.949	NK cells	post
MTRNR2L12	NA	-0.297388	0.00e+00	0.00e+00	0.952	0.979	NK cells	post
RPS26	ENSG00000197728	-0.879257	0.00e+00	0.00e+00	0.96	0.998	NK cells	post
VCAN	ENSG00000038427	0.30436	3.60e-40	7.70e-36	0.679	0.619	Mono/Macro	post
BRI3	ENSG00000164713	0.282122	0.00e+00	0.00e+00	0.84	0.766	Mono/Macro	post
TAF10	ENSG00000166337	0.260354	0.00e+00	0.00e+00	0.428	0.281	Mono/Macro	post
EFHD2	ENSG00000142634	0.255874	0.00e+00	0.00e+00	0.757	0.642	Mono/Macro	post
VIM	ENSG00000026025	0.251308	0.00e+00	0.00e+00	0.992	0.989	Mono/Macro	post
CEBPD	ENSG00000221869	0.250907	0.00e+00	0.00e+00	0.831	0.76	Mono/Macro	post
LYZ	ENSG00000090382	-0.270071	6.48e-27	1.39e-22	0.935	0.961	Mono/Macro	post

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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.

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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.)

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	7	186	0	23467	B cells	NA
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	11	186	0	23467	CD4+ T cells	NA
Regulation by the Disease Microenvironment	1.30e-01	1.30e-01	17	186	1	23467	CD8+ T cells	VIM
Regulation by the Disease Microenvironment	1.20e-01	1.20e-01	16	186	1	23467	cDCs	VIM
Regulation by the Disease Microenvironment	1.80e-01	1.80e-01	25	186	1	23467	Mono_Macro	VIM
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	18	186	0	23467	NK cells	NA
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	4	186	0	23467	pDCs	NA
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	5	186	0	23467	Plasma cells	NA

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.)

Up-regulated Hallmark	Up-regulated KEGG	Up-regulated GO BP

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.)

Down-regulated Hallmark	Down-regulated KEGG	Down-regulated GO BP

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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.)

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	1.50e-02	1.50e-02	24	186	2	23467	B cells	CXCR4,RHOB
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	6	186	0	23467	CD4+ T cells	NA
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	8	186	0	23467	CD8+ T cells	NA
Regulation by the Disease Microenvironment	1.30e-01	1.30e-01	18	186	1	23467	cDCs	CXCR4
Regulation by the Disease Microenvironment	8.40e-02	8.40e-02	11	186	1	23467	Mono_Macro	VIM
Regulation by the Disease Microenvironment	5.40e-02	5.40e-02	7	186	1	23467	NK cells	TGFB1
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	5	186	0	23467	pDCs	NA
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	31	186	0	23467	Plasma cells	NA

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.)

Up-regulated Hallmark	Up-regulated KEGG	Up-regulated GO BP

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.)

Down-regulated Hallmark	Down-regulated KEGG	Down-regulated GO BP

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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.)

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.)

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.)

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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.)

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

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.)

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

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.)

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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.)

Motifs and TFs regulating up-regulated DEGs in resistant group of the pre-treatment samples

motif	motif	NES	AUC	TF_highConf	Cell_type
	tfdimers__MD00035	11.1	0.848	MZF1; STAT6 (directAnnotation).	B cells
	transfac_pro__M05745	11.1	0.844	ZNF718 (directAnnotation).	B cells
	transfac_pro__M04814	10.7	0.816	RELA (directAnnotation).	B cells
	taipale_tf_pairs__HOXD12_ELK3_NTTTAYNNCCGGAARNN_CAP_repr	9.5	0.726	ELK3; HOXD12 (directAnnotation).	B cells
	transfac_pro__M06782	6.45	0.498	ZNF225 (directAnnotation).	B cells
	tfdimers__MD00542	6.42	0.496	E2F1; EBF1 (directAnnotation).	B cells
	transfac_pro__M05881	6.4	0.494	ZNF676 (directAnnotation).	B cells
	transfac_pro__M01239	6.39	0.494	RELA (directAnnotation).	B cells
	taipale_tf_pairs__TFAP2C_ONECUT2_NATCGATNNNNNNNNGCCTNNGGSNN_CAP_repr	6.34	0.49	ONECUT2; TFAP2C (directAnnotation).	B cells
	kznf__ZNF736_Imbeault2017_RP_RCADE	6.33	0.489	ZNF736 (directAnnotation).	B cells

Motifs and TFs regulating down-regulated DEGs in resistant group of the pre-treatment samples

motif	motif	NES	AUC	TF_highConf	Cell_type
	transfac_pro__M05706	6.59	0.387	ZNF20 (directAnnotation).	B cells
	taipale_tf_pairs__GCM2_DRGX_RTRSGGGNAATTAN_CAP_repr	5.79	0.343	DRGX; GCM2 (directAnnotation).	B cells
	transfac_pro__M06451	5.19	0.31	ZNF614 (directAnnotation).	B cells
	transfac_pro__M05520	5.12	0.307	E4F1 (inferredBy_Orthology).	B cells
	tfdimers__MD00386	4.59	0.277	GTF2IRD1; POU5F1 (directAnnotation).	B cells
	transfac_pro__M01694	4.55	0.275	YY2 (directAnnotation). MBTPS2 (inferredBy_Orthology).	B cells
	transfac_pro__M05756	4.38	0.266	ZNF470 (directAnnotation).	B cells
	taipale_tf_pairs__MEIS1_SOX2_TGACAKNNNAACAATGN_CAP_repr	4.37	0.265	MEIS1; SOX2 (directAnnotation).	B cells
	dbtfbs__SETDB1_HEK293_ENCSR348AGV_merged_N1	4.3	0.261	SETDB1 (directAnnotation).	B cells
	transfac_pro__M06391	4.15	0.253	ZNF836 (directAnnotation).	B cells

Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107

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.)

Motifs and TFs regulating up-regulated DEGs in resistant group of the post-treatment samples

motif	motif	NES	AUC	TF_highConf	Cell_type
	transfac_pro__M06609	5.4	0.275	ZKSCAN4 (directAnnotation).	B cells
	metacluster_5.1	5.36	0.273	HIVEP1; HIVEP1; NFAT5; NFKB1; NFKB1; NFKB1; NFKB1; NFKB1; NFKB1; NFKB1; NFKB1; NFKB1; NFKB2; NFKB2; NFKB2; NFKB2; NFKB2; REL; REL; REL; RELA; RELA; RELA; RELA; RELA; RELA; RELA; RELA; RELA; RELA; RELA; RELA; RELA; RELA; RELA; RELA; RELA; RELA; RELA; RELA; RELA; RELA; RELB; RELB (directAnnotation). NFAT5; NFKB1; NFKB1; NFKB1; NFKB1; NFKB1; NFKB2; NFKB2; NFKB2; REL; REL; REL; REL; RELA; RELA; RELA; RELA; RELA; RELB; RELB; RELB (inferredBy_Orthology).	B cells
	taipale_tf_pairs__TEAD4_DLX3_RCATTCCNNNNTAATKR_CAP	4.87	0.252	DLX3; TEAD4 (directAnnotation).	B cells
	tfdimers__MD00548	4.43	0.233	CEBPA; CEBPB; CEBPD; CEBPE; CEBPG; MYCN (directAnnotation).	B cells
	transfac_pro__M05509	4.38	0.231	PLAGL1 (directAnnotation).	B cells
	taipale_tf_pairs__TEAD4_HOXA3_RCATTCNNNNNNCATTA_CAP	4.33	0.229	HOXA3; TEAD4 (directAnnotation).	B cells
	tfdimers__MD00143	4.26	0.226	IKZF1; MZF1 (directAnnotation).	B cells
	metacluster_32.45	4.16	0.222	HDAC2 (directAnnotation).	B cells
	taipale_tf_pairs__TEAD4_HOXA3_RCATTCYNNNNNCATTA_CAP	4.13	0.221	HOXA3; TEAD4 (directAnnotation).	B cells
	tfdimers__MD00302	4.12	0.22	IRF7; IRF8 (directAnnotation).	B cells

Motifs and TFs regulating down-regulated DEGs in resistant group of the post-treatment samples

motif	motif	NES	AUC	TF_highConf	Cell_type
	metacluster_15.4	6.9	0.243	SMAD6 (directAnnotation). SMAD6 (inferredBy_Orthology).	B cells
	taipale_tf_pairs__HOXB2_PAX5_NNMATTAGTCACGCWTSRNTG_CAP	6.42	0.227	HOXB2; PAX5 (directAnnotation).	B cells
	metacluster_97.2	6.37	0.226	GTF3A (inferredBy_Orthology).	B cells
	tfdimers__MD00520	5.83	0.208	MYCN; MZF1 (directAnnotation).	B cells
	metacluster_178.20	5.21	0.188	ZKSCAN1 (directAnnotation). ZKSCAN1 (inferredBy_Orthology).	B cells
	kznf__ZNF613_Imbeault2017_RP_RCADE	5.16	0.186	ZNF613 (directAnnotation).	B cells
	transfac_pro__M06353	5.1	0.184	ZNF782 (directAnnotation).	B cells
	transfac_pro__M06092	5.05	0.182	ZNF28 (directAnnotation).	B cells
	taipale_tf_pairs__E2F3_DRGX_SGCGCTAATTKN_CAP_repr	4.96	0.18	DRGX; E2F3 (directAnnotation).	B cells
	metacluster_134.6	4.95	0.179	FOXF1; FOXG1; ZNF74 (directAnnotation). FOXG1 (inferredBy_Orthology).	B cells

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.)

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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
FOS	tfdimers__MD00090	down	CD4+ T cells	post
FOS	metacluster_137.5	up	CD4+ T cells	pre
JUN	metacluster_137.5	up	CD4+ T cells	pre
JUNB	metacluster_137.5	up	CD4+ T cells	pre
FOS	metacluster_137.2	up	CD4+ T cells	pre
JUN	metacluster_137.2	up	CD4+ T cells	pre
JUNB	metacluster_137.2	up	CD4+ T cells	pre
FOS	metacluster_157.2	up	CD4+ T cells	pre
JUN	metacluster_157.2	up	CD4+ T cells	pre
JUNB	metacluster_157.2	up	CD4+ T cells	pre

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