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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
H4C3	ENSG00000197061	0.266902	1.47e-13	3.67e-09	0.325	0.246	CD8+ T cells	pre
SELPLG	ENSG00000110876	0.266611	0.00e+00	0.00e+00	0.485	0.318	CD8+ T cells	pre
SASH3	ENSG00000122122	0.266426	0.00e+00	0.00e+00	0.312	0.145	CD8+ T cells	pre
CLEC2D	ENSG00000069493	0.266033	0.00e+00	0.00e+00	0.298	0.131	CD8+ T cells	pre
GZMM	ENSG00000197540	0.265634	2.80e-45	5.64e-41	0.666	0.519	CD8+ T cells	pre
SPN	ENSG00000197471	0.264618	0.00e+00	0.00e+00	0.386	0.215	CD8+ T cells	pre
MT2A	ENSG00000125148	0.263971	9.67e-16	2.41e-11	0.677	0.727	CD8+ T cells	pre
PRDX1	ENSG00000117450	0.263183	0.00e+00	0.00e+00	0.347	0.189	CD8+ T cells	pre
FAM107B	ENSG00000065809	0.262329	0.00e+00	0.00e+00	0.386	0.203	CD8+ T cells	pre
SH3BGRL3	ENSG00000142669	0.260955	0.00e+00	0.00e+00	0.998	0.998	CD8+ T cells	pre
ARL6IP5	ENSG00000144746	0.259134	0.00e+00	0.00e+00	0.745	0.602	CD8+ T cells	pre
SLFN5	ENSG00000166750	0.258922	0.00e+00	0.00e+00	0.331	0.158	CD8+ T cells	pre
S100A4	ENSG00000196154	0.258768	0.00e+00	0.00e+00	0.989	0.991	CD8+ T cells	pre
MT-ATP6	ENSG00000198899	0.256552	0.00e+00	0.00e+00	0.999	0.994	CD8+ T cells	pre
VIM	ENSG00000026025	0.255525	4.23e-28	1.05e-23	0.975	0.975	CD8+ T cells	pre
TRAF3IP3	ENSG00000009790	0.253986	0.00e+00	0.00e+00	0.519	0.341	CD8+ T cells	pre
M6PR	ENSG00000003056	0.253583	0.00e+00	0.00e+00	0.353	0.182	CD8+ T cells	pre
HMGB2	ENSG00000164104	0.253048	6.36e-14	1.58e-09	0.455	0.387	CD8+ T cells	pre
HNRNPF	ENSG00000169813	0.252644	0.00e+00	0.00e+00	0.381	0.223	CD8+ T cells	pre
ANXA1	ENSG00000135046	0.252438	7.44e-28	1.85e-23	0.799	0.817	CD8+ T cells	pre
PTPRC	ENSG00000262418	0.251214	0.00e+00	0.00e+00	0.955	0.95	CD8+ T cells	pre
ARHGAP30	ENSG00000186517	0.250012	0.00e+00	0.00e+00	0.387	0.214	CD8+ T cells	pre
KLF3	ENSG00000109787	-0.252665	2.57e-19	6.39e-15	0.412	0.445	CD8+ T cells	pre
HLA-DRB5	ENSG00000198502	-0.255404	1.65e-25	4.11e-21	0.375	0.449	CD8+ T cells	pre
CEBPB	ENSG00000172216	-0.259561	8.66e-35	2.16e-30	0.241	0.333	CD8+ T cells	pre
FTH1	ENSG00000167996	-0.265306	0.00e+00	0.00e+00	0.998	0.998	CD8+ T cells	pre
RBM39	ENSG00000131051	-0.269359	7.54e-42	1.88e-37	0.704	0.806	CD8+ T cells	pre
RPS14	ENSG00000164587	-0.27479	0.00e+00	0.00e+00	0.999	0.999	CD8+ T cells	pre
YBX3	ENSG00000060138	-0.286885	5.23e-31	1.30e-26	0.217	0.302	CD8+ T cells	pre
HERPUD1	ENSG00000051108	-0.290086	2.16e-27	5.37e-23	0.361	0.427	CD8+ T cells	pre
CCNH	ENSG00000134480	-0.291775	2.42e-24	6.02e-20	0.246	0.305	CD8+ T cells	pre
UBB	ENSG00000170315	-0.311506	2.19e-35	5.45e-31	0.901	0.957	CD8+ T cells	pre
JUND	ENSG00000130522	-0.315105	0.00e+00	0.00e+00	0.634	0.828	CD8+ T cells	pre
EIF1	ENSG00000173812	-0.360257	0.00e+00	0.00e+00	0.998	0.999	CD8+ T cells	pre
SPON2	ENSG00000159674	-0.362631	7.69e-34	1.92e-29	0.209	0.293	CD8+ T cells	pre
NFKBIA	ENSG00000100906	-0.367638	0.00e+00	0.00e+00	0.629	0.83	CD8+ T cells	pre
DDIT4	ENSG00000168209	-0.369206	0.00e+00	0.00e+00	0.438	0.576	CD8+ T cells	pre
SLC25A39	ENSG00000013306	-0.370006	3.08e-15	7.67e-11	0.325	0.36	CD8+ T cells	pre
ZFP36L2	ENSG00000152518	-0.402127	0.00e+00	0.00e+00	0.94	0.978	CD8+ T cells	pre
TYROBP	ENSG00000011600	-0.414096	0.00e+00	0.00e+00	0.278	0.495	CD8+ T cells	pre
SLC25A37	ENSG00000147454	-0.431482	0.00e+00	0.00e+00	0.17	0.288	CD8+ T cells	pre
RBM38	ENSG00000132819	-0.438858	0.00e+00	0.00e+00	0.285	0.404	CD8+ T cells	pre
BTG1	ENSG00000133639	-0.443455	0.00e+00	0.00e+00	0.946	0.979	CD8+ T cells	pre
CXCR4	ENSG00000121966	-0.446356	0.00e+00	0.00e+00	0.672	0.834	CD8+ T cells	pre
TNFAIP3	ENSG00000118503	-0.464238	0.00e+00	0.00e+00	0.621	0.796	CD8+ T cells	pre
ALAS2	ENSG00000158578	-0.468935	0.00e+00	0.00e+00	0.138	0.258	CD8+ T cells	pre
TSC22D3	ENSG00000157514	-0.508172	0.00e+00	0.00e+00	0.772	0.924	CD8+ T cells	pre
DUSP1	ENSG00000120129	-0.53204	0.00e+00	0.00e+00	0.584	0.851	CD8+ T cells	pre
JUN	ENSG00000177606	-0.533228	0.00e+00	0.00e+00	0.499	0.785	CD8+ T cells	pre
RPL13P12	ENSG00000215030	-0.55085	0.00e+00	0.00e+00	0.382	0.651	CD8+ T 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
HLA-H	ENSG00000231904	1.16261	0.00e+00	0.00e+00	0.55	0.17	NK cells	post
IFITM3	ENSG00000142089	0.564237	1.27e-29	3.17e-25	0.683	0.595	NK cells	post
AL365357.1	NA	0.509486	0.00e+00	0.00e+00	0.36	0.056	NK cells	post
MAP3K8	ENSG00000107968	0.43683	4.20e-45	1.19e-40	0.741	0.636	NK cells	post
GZMK	ENSG00000113088	0.430681	4.34e-23	1.08e-18	0.349	0.23	NK cells	post
RPS26	ENSG00000197728	0.421984	0.00e+00	0.00e+00	0.997	0.998	NK cells	post
HLA-DQB1	ENSG00000206237	0.421695	8.41e-45	2.05e-40	0.387	0.22	NK cells	post
HLA-DRB1	ENSG00000228080	0.418726	8.11e-36	2.02e-31	0.825	0.775	NK cells	post
HLA-DPB1	ENSG00000236693	0.383963	8.25e-38	2.06e-33	0.786	0.716	NK cells	post
PIK3R1	ENSG00000145675	0.369507	3.81e-37	9.49e-33	0.762	0.683	NK cells	post
AREG	ENSG00000109321	0.36486	7.44e-22	1.85e-17	0.413	0.298	NK cells	post
RPS9	ENSG00000274646	0.358826	0.00e+00	0.00e+00	0.999	0.995	NK cells	post
LAIR1	ENSG00000276163	0.358775	9.77e-15	2.43e-10	0.414	0.356	NK cells	post
IFITM1	ENSG00000185885	0.343255	5.11e-39	1.27e-34	0.991	0.989	NK cells	post
GSTP1	ENSG00000084207	0.338009	4.20e-44	1.03e-39	0.936	0.912	NK cells	post
ACTB	ENSG00000075624	0.333456	0.00e+00	0.00e+00	1	1	NK cells	post
MT-ND1	ENSG00000198888	0.331557	0.00e+00	0.00e+00	0.994	0.98	NK cells	post
COTL1	ENSG00000103187	0.330824	4.74e-19	1.18e-14	0.557	0.454	NK cells	post
PSME2	ENSG00000284889	0.318925	5.24e-41	1.31e-36	0.873	0.853	NK cells	post
MT-ATP6	ENSG00000198899	0.301959	0.00e+00	0.00e+00	1	1	NK cells	post
PRMT2	ENSG00000160310	0.298733	2.61e-32	6.49e-28	0.586	0.469	NK cells	post
KIR2DL3	ENSG00000273947	0.290935	7.03e-29	1.75e-24	0.272	0.142	NK cells	post
CALR	ENSG00000179218	0.284402	2.40e-22	5.96e-18	0.856	0.817	NK cells	post
MT-ATP8	ENSG00000228253	0.278108	1.76e-36	4.40e-32	0.93	0.899	NK cells	post
CD7	ENSG00000173762	0.276203	3.78e-22	9.40e-18	0.914	0.938	NK cells	post
HOPX	ENSG00000171476	0.26884	4.57e-23	1.14e-18	0.873	0.834	NK cells	post
CNN2	ENSG00000064666	0.268206	7.03e-24	1.75e-19	0.759	0.698	NK cells	post
FTH1	ENSG00000167996	0.264868	5.36e-25	1.34e-20	0.995	0.994	NK cells	post
RPS2	ENSG00000140988	0.258523	0.00e+00	3.60e-43	0.999	0.996	NK cells	post
HLA-A	ENSG00000227715	0.253603	0.00e+00	0.00e+00	1	1	NK cells	post
ARHGAP25	ENSG00000163219	-0.250204	2.58e-43	6.41e-39	0.223	0.387	NK cells	post
CDC42SE1	ENSG00000197622	-0.253376	1.15e-35	2.85e-31	0.457	0.621	NK cells	post
ARHGAP9	ENSG00000123329	-0.253936	2.22e-31	5.52e-27	0.65	0.772	NK cells	post
PTGER4	ENSG00000171522	-0.255447	1.00e-30	2.49e-26	0.327	0.472	NK cells	post
SH2D1B	ENSG00000198574	-0.255971	5.93e-26	1.48e-21	0.307	0.423	NK cells	post
MT-RNR2	ENSG00000210082	-0.25692	3.66e-29	9.12e-25	1	1	NK cells	post
MT1E	ENSG00000169715	-0.257106	3.18e-32	7.91e-28	0.22	0.356	NK cells	post
MAT2B	ENSG00000038274	-0.257592	2.10e-44	5.20e-40	0.266	0.44	NK cells	post
SASH3	ENSG00000122122	-0.260397	1.28e-33	3.19e-29	0.51	0.654	NK cells	post
AL138963.4	NA	-0.260611	1.17e-35	2.91e-31	0.219	0.363	NK cells	post
PPP1R12A	ENSG00000058272	-0.261219	1.54e-34	3.85e-30	0.447	0.599	NK cells	post
RPL13P12	ENSG00000215030	-0.262181	0.00e+00	0.00e+00	0.284	0.52	NK cells	post
PRF1	ENSG00000180644	-0.264798	2.05e-35	5.10e-31	0.988	0.994	NK cells	post
RPS2P5	ENSG00000240342	-0.267246	5.66e-39	1.41e-34	0.827	0.907	NK cells	post
AKR1C3	ENSG00000196139	-0.270377	2.16e-37	5.38e-33	0.178	0.322	NK cells	post
ARL6IP5	ENSG00000144746	-0.270441	3.66e-42	9.11e-38	0.625	0.79	NK cells	post
IKZF3	ENSG00000161405	-0.27153	7.64e-40	1.90e-35	0.281	0.442	NK cells	post
ANXA1	ENSG00000135046	-0.272959	8.86e-28	2.21e-23	0.751	0.851	NK cells	post
YPEL3	ENSG00000090238	-0.274368	3.75e-39	9.34e-35	0.625	0.774	NK cells	post
FOSB	ENSG00000125740	-0.274509	2.36e-35	5.87e-31	0.327	0.484	NK 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

Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

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

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

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

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

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."