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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: GSE197268_Tisa-cel

Dataset summary for GSE197268_Tisa-cel

Datast information	Dataset	GSE197268_Tisa-cel
	PMID	36097221
	Raw data ID/link	phs002922.v1.p1
	Organism	Homo sapiens
	Source	patients
	Tissue	Peripheral blood mononuclear cells
	Cancer type level1	Acute lymphoblastic leukemia
	Cancer type level2	Large B-cell acute lymphoblastic leukemia (B-ALL)
	Regimen	tisa-cel (CAR-T)
	Drug type	Immunotherapy
	Sample size	pre (resistant 4, sensitive 2); post (resistant 8, sensitive 5)
	Cell number	157733
	Extract protocol	10x genomics
	Data processing	CellRanger 6.0.1
	Public date	Public on Jul 13, 2022
	Description	This dataset has 13 patients, 6 of whom has both pre- and post-treatment samples.

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Drug summary for GSE197268_Tisa-cel

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"tisa-cel (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.)

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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
S100B	ENSG00000160307	1.50627	0.00e+00	0.00e+00	0.385	0.012	NK cells	pre
HLA-H	ENSG00000231904	1.33037	0.00e+00	0.00e+00	0.684	0.102	NK cells	pre
MYOM2	ENSG00000274137	0.915394	0.00e+00	0.00e+00	0.369	0.003	NK cells	pre
XCL2	ENSG00000143185	0.910131	0.00e+00	0.00e+00	0.32	0.036	NK cells	pre
AL365357.1	NA	0.834196	0.00e+00	0.00e+00	0.397	0.004	NK cells	pre
SELL	ENSG00000188404	0.745613	0.00e+00	0.00e+00	0.35	0.063	NK cells	pre
CD81	ENSG00000110651	0.721942	0.00e+00	0.00e+00	0.818	0.494	NK cells	pre
GZMB	ENSG00000100453	0.666895	0.00e+00	0.00e+00	0.979	0.976	NK cells	pre
CD2	ENSG00000116824	0.652147	0.00e+00	0.00e+00	0.517	0.172	NK cells	pre
RPS26	ENSG00000197728	0.638709	0.00e+00	0.00e+00	0.986	1	NK cells	pre
MT-ATP6	ENSG00000198899	0.631888	0.00e+00	0.00e+00	1	1	NK cells	pre
CD52	ENSG00000169442	0.618609	0.00e+00	0.00e+00	0.954	0.995	NK cells	pre
GNLY	ENSG00000115523	0.583846	0.00e+00	0.00e+00	0.996	1	NK cells	pre
KLRF1	ENSG00000150045	0.577322	0.00e+00	0.00e+00	0.624	0.347	NK cells	pre
GIMAP7	ENSG00000179144	0.572377	0.00e+00	0.00e+00	0.585	0.254	NK cells	pre
KLRG1	ENSG00000139187	0.556946	0.00e+00	0.00e+00	0.332	0.051	NK cells	pre
IL2RB	ENSG00000100385	0.535886	1.37e-33	3.40e-29	0.67	0.445	NK cells	pre
PLEK	ENSG00000115956	0.523889	0.00e+00	0.00e+00	0.644	0.321	NK cells	pre
MT-ND3	ENSG00000198840	0.508421	0.00e+00	0.00e+00	0.993	0.997	NK cells	pre
CX3CR1	ENSG00000168329	0.507297	2.10e-44	5.24e-40	0.503	0.234	NK cells	pre
CCL4	ENSG00000277943	0.499635	3.89e-24	9.69e-20	0.537	0.327	NK cells	pre
LAIR1	ENSG00000276163	0.496737	0.00e+00	0.00e+00	0.422	0.144	NK cells	pre
GIMAP4	ENSG00000133574	0.488394	0.00e+00	0.00e+00	0.426	0.127	NK cells	pre
FCER1G	ENSG00000158869	0.481899	1.07e-28	2.67e-24	0.72	0.593	NK cells	pre
GZMA	ENSG00000145649	0.479971	0.00e+00	0.00e+00	0.979	0.99	NK cells	pre
RPS27	ENSG00000177954	0.472654	0.00e+00	0.00e+00	1	1	NK cells	pre
APOBEC3G	ENSG00000239713	0.468621	0.00e+00	0.00e+00	0.511	0.214	NK cells	pre
KLRD1	ENSG00000134539	0.456174	0.00e+00	0.00e+00	0.871	0.586	NK cells	pre
ITGB1	ENSG00000150093	0.449878	4.42e-36	1.10e-31	0.541	0.308	NK cells	pre
MTATP6P1	ENSG00000248527	0.424999	2.91e-38	7.25e-34	0.75	0.583	NK cells	pre
XBP1	ENSG00000100219	0.424935	6.95e-43	1.73e-38	0.609	0.316	NK cells	pre
MT-CO1	ENSG00000198804	0.417208	0.00e+00	0.00e+00	1	1	NK cells	pre
MT-CYB	ENSG00000198727	0.409877	0.00e+00	0.00e+00	1	1	NK cells	pre
PRSS23	ENSG00000150687	0.406239	7.20e-31	1.79e-26	0.493	0.265	NK cells	pre
TRDC	ENSG00000211829	0.401272	6.07e-32	1.51e-27	0.41	0.221	NK cells	pre
RPS29	ENSG00000213741	0.398434	7.57e-44	1.88e-39	0.945	0.991	NK cells	pre
RPS4X	ENSG00000198034	0.391546	0.00e+00	0.00e+00	1	1	NK cells	pre
CMC1	ENSG00000187118	0.389851	5.64e-22	1.40e-17	0.619	0.427	NK cells	pre
RIPOR2	ENSG00000111913	0.375975	2.06e-40	5.12e-36	0.559	0.266	NK cells	pre
CD300A	ENSG00000167851	0.374565	0.00e+00	9.53e-44	0.397	0.13	NK cells	pre
MT-ND4	ENSG00000198886	0.365669	1.06e-43	2.66e-39	0.999	1	NK cells	pre
PRMT2	ENSG00000160310	0.360837	2.99e-38	7.44e-34	0.599	0.307	NK cells	pre
IFITM3	ENSG00000142089	0.358946	6.35e-09	1.58e-04	0.695	0.841	NK cells	pre
SPOCK2	ENSG00000107742	0.353588	1.15e-26	2.86e-22	0.35	0.164	NK cells	pre
MAP2K2	ENSG00000126934	0.344479	3.31e-41	8.24e-37	0.479	0.201	NK cells	pre
HOPX	ENSG00000171476	0.344292	2.76e-24	6.86e-20	0.811	0.68	NK cells	pre
AC004687.1	NA	0.33676	3.75e-32	9.34e-28	0.506	0.252	NK cells	pre
CDK2AP2	ENSG00000167797	0.333577	1.31e-36	3.26e-32	0.497	0.228	NK cells	pre
FAM107B	ENSG00000065809	0.331205	2.84e-37	7.07e-33	0.424	0.174	NK cells	pre
RPS18	ENSG00000223367	0.330323	1.64e-32	4.08e-28	1	1	NK cells	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
S100A10	ENSG00000197747	-0.314696	0.00e+00	0.00e+00	0.939	0.973	CD8+ T cells	post
HLA-DRB5	ENSG00000198502	-0.351947	0.00e+00	0.00e+00	0.557	0.644	CD8+ T cells	post
PPP1R15A	ENSG00000087074	-0.387654	0.00e+00	0.00e+00	0.385	0.555	CD8+ T cells	post
CD27	ENSG00000139193	-0.391305	0.00e+00	0.00e+00	0.308	0.456	CD8+ T cells	post
GPX1	ENSG00000233276	-0.41609	0.00e+00	0.00e+00	0.244	0.392	CD8+ T cells	post
KLF6	ENSG00000067082	-0.530182	0.00e+00	0.00e+00	0.596	0.781	CD8+ T cells	post
FOS	ENSG00000170345	-0.760972	0.00e+00	0.00e+00	0.491	0.75	CD8+ T cells	post
ITM2C	ENSG00000135916	0.959073	0.00e+00	0.00e+00	0.453	0.207	CD4+ T cells	post
HLA-H	ENSG00000231904	0.716115	0.00e+00	0.00e+00	0.489	0.136	CD4+ T cells	post
HLA-DQB1	ENSG00000206237	0.64311	0.00e+00	0.00e+00	0.494	0.184	CD4+ T cells	post
STAT1	ENSG00000115415	0.621942	0.00e+00	0.00e+00	0.538	0.274	CD4+ T cells	post
IFITM3	ENSG00000142089	0.576845	0.00e+00	0.00e+00	0.652	0.469	CD4+ T cells	post
IFITM1	ENSG00000185885	0.541543	0.00e+00	0.00e+00	0.99	0.984	CD4+ T cells	post
HLA-C	ENSG00000206435	0.498443	0.00e+00	0.00e+00	1	1	CD4+ T cells	post
ISG15	ENSG00000187608	0.489237	0.00e+00	0.00e+00	0.585	0.429	CD4+ T cells	post
TGFB1	ENSG00000105329	0.415161	0.00e+00	0.00e+00	0.927	0.896	CD4+ T cells	post
IFI6	ENSG00000126709	0.387131	0.00e+00	0.00e+00	0.435	0.292	CD4+ T cells	post
AL138963.4	NA	0.37838	0.00e+00	0.00e+00	0.451	0.29	CD4+ T cells	post
SMAP2	ENSG00000084070	0.340979	0.00e+00	0.00e+00	0.561	0.35	CD4+ T cells	post
MX1	ENSG00000157601	0.339392	0.00e+00	0.00e+00	0.3	0.155	CD4+ T cells	post
H1-10	ENSG00000184897	0.326942	0.00e+00	0.00e+00	0.707	0.633	CD4+ T cells	post
RBM38	ENSG00000132819	0.315768	0.00e+00	0.00e+00	0.698	0.523	CD4+ T cells	post
LY6E	ENSG00000278032	0.313946	0.00e+00	0.00e+00	0.949	0.951	CD4+ T cells	post
TAP1	ENSG00000232367	0.312654	0.00e+00	0.00e+00	0.627	0.459	CD4+ T cells	post
ISG20	ENSG00000172183	0.311743	0.00e+00	0.00e+00	0.779	0.657	CD4+ T cells	post
RPS2P5	ENSG00000240342	0.307293	0.00e+00	0.00e+00	0.933	0.933	CD4+ T cells	post
XAF1	ENSG00000132530	0.30276	0.00e+00	0.00e+00	0.349	0.202	CD4+ T cells	post
GBP5	ENSG00000154451	0.284288	0.00e+00	0.00e+00	0.451	0.336	CD4+ T cells	post
GSPT1	ENSG00000103342	0.2839	0.00e+00	0.00e+00	0.632	0.477	CD4+ T cells	post
EPSTI1	ENSG00000133106	0.283467	0.00e+00	0.00e+00	0.259	0.111	CD4+ T cells	post
SLFN5	ENSG00000166750	0.280393	0.00e+00	0.00e+00	0.491	0.316	CD4+ T cells	post
TXNIP	ENSG00000265972	0.279684	0.00e+00	0.00e+00	0.96	0.942	CD4+ T cells	post
UBE2L6	ENSG00000156587	0.279278	0.00e+00	0.00e+00	0.637	0.473	CD4+ T cells	post
AL365357.1	NA	0.275396	0.00e+00	0.00e+00	0.25	0.108	CD4+ T cells	post
RNF213	ENSG00000173821	0.270284	0.00e+00	0.00e+00	0.66	0.525	CD4+ T cells	post
IL7R	ENSG00000168685	0.268906	0.00e+00	0.00e+00	0.865	0.782	CD4+ T cells	post
RHBDD2	ENSG00000005486	0.267423	0.00e+00	0.00e+00	0.599	0.451	CD4+ T cells	post
GBP1	ENSG00000117228	0.26458	0.00e+00	0.00e+00	0.274	0.135	CD4+ T cells	post
BCL3	ENSG00000069399	0.258709	0.00e+00	0.00e+00	0.45	0.282	CD4+ T cells	post
GNAS	ENSG00000087460	0.256099	0.00e+00	0.00e+00	0.875	0.84	CD4+ T cells	post
FKBP5	ENSG00000096060	0.251797	0.00e+00	0.00e+00	0.289	0.125	CD4+ T cells	post
RPS3A	ENSG00000145425	-0.271116	0.00e+00	0.00e+00	0.999	0.999	CD4+ T cells	post
HSP90AB1	ENSG00000096384	-0.272664	0.00e+00	0.00e+00	0.832	0.889	CD4+ T cells	post
MT-ND1	ENSG00000198888	-0.274892	0.00e+00	0.00e+00	0.984	0.992	CD4+ T cells	post
CD7	ENSG00000173762	-0.2758	0.00e+00	0.00e+00	0.645	0.719	CD4+ T cells	post
GZMA	ENSG00000145649	-0.278862	0.00e+00	0.00e+00	0.678	0.777	CD4+ T cells	post
CXCR4	ENSG00000121966	-0.281446	0.00e+00	0.00e+00	0.735	0.788	CD4+ T cells	post
MT-ND4L	ENSG00000212907	-0.296582	0.00e+00	0.00e+00	0.981	0.98	CD4+ T cells	post
JUN	ENSG00000177606	-0.296793	0.00e+00	0.00e+00	0.767	0.838	CD4+ T cells	post
MT-ATP8	ENSG00000228253	-0.32596	0.00e+00	0.00e+00	0.891	0.923	CD4+ T cells	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	2.00e-02	2.00e-02	130	186	4	23467	CD4+ T cells	BCL2,MYC,TGFB1,SOCS3
Regulation by the Disease Microenvironment	3.20e-01	3.20e-01	146	186	2	23467	CD8+ T cells	CXCR4,VIM
Regulation by the Disease Microenvironment	4.60e-02	4.60e-02	326	186	6	23467	Mono_Macro	PAK1,CX3CR1,CXCR4,SOCS3,VIM,TIMP2
Regulation by the Disease Microenvironment	8.90e-02	8.90e-02	133	186	3	23467	NK cells	TGFB1,CX3CR1,CXCR4

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	6.00e-02	6.00e-02	50	186	2	23467	CD4+ T cells	TGFB1,CXCR4
Regulation by the Disease Microenvironment	3.10e-02	3.10e-02	35	186	2	23467	CD8+ T cells	TGFB1,VIM
Regulation by the Disease Microenvironment	3.70e-01	3.70e-01	58	186	1	23467	Mono_Macro	IL1B
Regulation by the Disease Microenvironment	6.00e-01	6.00e-01	114	186	1	23467	NK cells	CX3CR1

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
	transfac_pro__M06260	4.32	0.0931	ZNF91 (directAnnotation).	CD4+ T cells
	transfac_pro__M06117	4.29	0.0926	ZNF23 (directAnnotation).	CD4+ T cells
	taipale__MYBL2_DBD_AACCGTTAACGGNN	4.14	0.0903	MYBL2 (directAnnotation).	CD4+ T cells
	transfac_pro__M06251	3.94	0.0871	ZSCAN2 (inferredBy_Orthology).	CD4+ T cells
	kznf__ZNF181_Imbeault2017_OM_RCADE	3.72	0.0838	ZNF181 (directAnnotation).	CD4+ T cells
	transfac_pro__M06721	3.62	0.0822	ZKSCAN7 (directAnnotation).	CD4+ T cells
	transfac_pro__M05626	3.49	0.0801	ZNF780A (directAnnotation).	CD4+ T cells
	kznf__ZBTB14_Schmitges2016_RCADE	3.35	0.078	ZBTB14 (directAnnotation).	CD4+ T cells
	transfac_pro__M05392	3.29	0.077	SCRT2 (inferredBy_Orthology).	CD4+ T cells
	metacluster_172.19	3.28	0.0769	HMGA2 (directAnnotation).	CD4+ T cells

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

motif	motif	NES	AUC	TF_highConf	Cell_type
	taipale_tf_pairs__FOXJ2_PITX1_NTAATCCNNWMAACA_CAP_repr	5.97	0.156	FOXJ2; PITX1 (directAnnotation).	CD4+ T cells
	transfac_pro__M05744	4.42	0.122	ZXDC (directAnnotation).	CD4+ T cells
	transfac_public__M00266	4.39	0.121	FOXC2 (inferredBy_Orthology).	CD4+ T cells
	transfac_pro__M06129	4.22	0.118	GLI4 (directAnnotation).	CD4+ T cells
	metacluster_91.4	4.02	0.113	GZF1; HSFY2 (directAnnotation).	CD4+ T cells
	metacluster_77.10	3.97	0.112	SRY (inferredBy_Orthology).	CD4+ T cells
	metacluster_22.21	3.95	0.112	NFE2L2 (inferredBy_Orthology).	CD4+ T cells
	metacluster_130.18	3.92	0.111	FOXD2; FOXD2 (directAnnotation). FOXA2; FOXD2; FOXD2 (inferredBy_Orthology).	CD4+ T cells
	metacluster_179.5	3.88	0.11	MEF2A; MEF2A; MEF2A; MEF2A (directAnnotation).	CD4+ T cells
	tfdimers__MD00187	3.86	0.11	GATA1; GATA2; GATA3; GATA4; GATA5; GATA6 (directAnnotation).	CD4+ T cells

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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
	metacluster_2.6	6.94	0.208	IRF1; IRF1; IRF1; IRF1; IRF1; IRF1; IRF1; IRF1; IRF1; IRF1; IRF2; IRF2; IRF2; IRF2; IRF2; IRF2; IRF2; IRF3; IRF3; IRF3; IRF3; IRF3; IRF3; IRF4; IRF4; IRF4; IRF4; IRF4; IRF5; IRF5; IRF5; IRF5; IRF5; IRF5; IRF5; IRF6; IRF7; IRF7; IRF7; IRF7; IRF7; IRF7; IRF7; IRF8; IRF8; IRF8; IRF8; IRF8; IRF8; IRF8; IRF8; IRF9; IRF9; IRF9; IRF9; IRF9; IRF9; IRF9; STAT1; STAT2; STAT2; STAT2; STAT2; ZNF426; ZNF71 (directAnnotation). IRF1; IRF1; IRF3; IRF8 (inferredBy_Orthology).	CD4+ T cells
	metacluster_2.9	6.88	0.207	IRF2; IRF2; IRF2; PRDM1; PRDM1 (directAnnotation). PRDM1 (inferredBy_Orthology).	CD4+ T cells
	metacluster_2.8	6.34	0.193	IRF4; IRF5; IRF6; IRF9 (directAnnotation). IRF3; IRF5; IRF5; IRF6 (inferredBy_Orthology).	CD4+ T cells
	tfdimers__MD00007	6.07	0.187	E2F1; IRF8 (directAnnotation).	CD4+ T cells
	metacluster_2.7	5.49	0.172	IRF1; IRF1; IRF2; IRF2; IRF3; IRF4; IRF5; IRF6; IRF7; IRF7; IRF8; IRF8; IRF9; PRDM1; PRDM1; PRDM1; PRDM1; PRDM1; PRDM1; PRDM1; PRDM1; PRDM1; PRDM1; PRDM1; PRDM1; STAT1; STAT1; STAT2 (directAnnotation). PRDM1; PRDM1; PRDM1 (inferredBy_Orthology).	CD4+ T cells
	transfac_pro__M06160	5.11	0.162	ZNF92 (directAnnotation).	CD4+ T cells
	transfac_pro__M05550	4.9	0.157	SNAPC4 (inferredBy_Orthology).	CD4+ T cells
	taipale__IRF7_DBD_RAANCGAAAWTCGNTTY_repr	4.77	0.154	IRF7 (directAnnotation).	CD4+ T cells
	jaspar__MA1509.1	4.72	0.152	IRF6 (directAnnotation).	CD4+ T cells
	transfac_pro__M04887	4.58	0.149	TCF12 (directAnnotation).	CD4+ T cells

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

motif	motif	NES	AUC	TF_highConf	Cell_type
	kznf__ZNF45_Imbeault2017_OM_RCADE	6.23	0.236	ZNF45 (directAnnotation).	CD4+ T cells
	metacluster_168.5	4.99	0.194	ZNF768; ZNF768 (directAnnotation).	CD4+ T cells
	transfac_pro__M05765	4.88	0.19	ZNF684 (directAnnotation).	CD4+ T cells
	homer__RHHCAGAGAGGB_ZNF768	4.85	0.189	ZNF768 (directAnnotation).	CD4+ T cells
	transfac_pro__M06129	4.8	0.187	GLI4 (directAnnotation).	CD4+ T cells
	swissregulon__hs__UBP1	4.78	0.187	UBP1 (directAnnotation).	CD4+ T cells
	transfac_pro__M06292	4.64	0.182	ZNF766 (directAnnotation).	CD4+ T cells
	metacluster_97.2	4.53	0.178	GTF3A (inferredBy_Orthology).	CD4+ T cells
	metacluster_91.4	4.34	0.172	GZF1; HSFY2 (directAnnotation).	CD4+ T cells
	taipale_cyt_meth__ZNF385D_NCGTCGCGACGN_eDBD_repr	4.24	0.168	ZNF385D (directAnnotation).	CD4+ T cells

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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. 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
STAT1	metacluster_2.6	up	CD4+ T cells	post
STAT1	metacluster_2.7	up	CD4+ T cells	post
FOS	metacluster_50.1	down	CD4+ T cells	post
JUN	metacluster_50.1	down	CD4+ T cells	post
FOS	tfdimers__MD00036	down	CD4+ T cells	post
JUN	tfdimers__MD00036	down	CD4+ T cells	post
STAT1	tfdimers__MD00230	up	CD8+ T cells	post
IRF1	metacluster_2.6	up	CD8+ T cells	post
STAT1	metacluster_2.6	up	CD8+ T cells	post
FOS	tfdimers__MD00230	down	CD8+ T cells	post

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1	"Sun X, Zhang Y, Li H, Zhou Y, Shi S, Chen Z, He X, Zhang H, Li F, Yin J, Mou M, Wang Y, Qiu Y, Zhu F. DRESIS: the first comprehensive landscape of drug resistance information. Nucleic Acids Res. 2023 Jan 6;51(D1):D1263-D1275. doi: 10.1093/nar/gkac812. PMID: 36243960; PMCID: PMC9825618."
2	"Wishart DS, Feunang YD, Guo AC, Lo EJ, Marcu A, Grant JR, Sajed T, Johnson D, Li C, Sayeeda Z, Assempour N, Iynkkaran I, Liu Y, Maciejewski A, Gale N, Wilson A, Chin L, Cummings R, Le D, Pon A, Knox C, Wilson M. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res. 2018 Jan 4;46(D1):D1074-D1082. doi: 10.1093/nar/gkx1037. PMID: 29126136; PMCID: PMC5753335."