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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
	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: GSE162117

Dataset summary for GSE162117

Datast information	Dataset	GSE162117
	PMID	34514432
	Raw data ID/link	PRJNA680611
	Organism	Homo sapiens
	Source	patients
	Tissue	Peripheral blood mononuclear cells
	Cancer type level1	Acute myeloid leukemia
	Cancer type level2	Tefractory acute myeloid leukemia (AML)
	Regimen	ficlatuzumab
	Drug type	Targeted therapy
	Sample size	pre (resistant 4, sensitive 7); post (resistant 3, sensitive 6)
	Cell number	43486
	Extract protocol	10x genomics
	Data processing	CellRanger 2.0.1
	Public date	Public on Sep 03, 2021
	Description	This dataset has 11 patients, 9 of whom have both pre- and post-treatment samples.

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Drug summary for GSE162117

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"ficlatuzumab" 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.)

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
RPL36A	ENSG00000241343	0.62492	4.57e-20	8.44e-16	0.884	0.7	NK cells	pre
RPS29	ENSG00000213741	0.619981	1.22e-32	2.25e-28	1	1	NK cells	pre
MT-ND3	ENSG00000198840	0.596179	6.66e-24	1.23e-19	1	0.987	NK cells	pre
IFITM3	ENSG00000142089	0.573961	1.97e-11	3.64e-07	0.378	0.173	NK cells	pre
RPS28	ENSG00000233927	0.560697	7.09e-33	1.31e-28	1	1	NK cells	pre
RPS21	ENSG00000171858	0.506809	2.88e-22	5.33e-18	1	0.992	NK cells	pre
DONSON	ENSG00000159147	0.482524	1.38e-18	2.54e-14	0.489	0.195	NK cells	pre
RPL37	ENSG00000145592	0.479432	3.21e-29	5.94e-25	1	1	NK cells	pre
RPL38	ENSG00000172809	0.441247	7.74e-18	1.43e-13	0.996	0.99	NK cells	pre
RPL39	ENSG00000198918	0.429866	8.94e-22	1.65e-17	1	1	NK cells	pre
RPS4Y1	ENSG00000129824	0.422802	4.93e-12	9.12e-08	0.689	0.429	NK cells	pre
RPL37A	ENSG00000197756	0.42209	2.83e-21	5.23e-17	1	1	NK cells	pre
XCL2	ENSG00000143185	0.419312	1.14e-06	2.11e-02	0.302	0.164	NK cells	pre
RPS27	ENSG00000177954	0.406284	7.72e-16	1.43e-11	1	1	NK cells	pre
RPL36	ENSG00000130255	0.401736	5.91e-18	1.09e-13	1	0.99	NK cells	pre
IFITM2	ENSG00000185201	0.390679	1.66e-07	3.07e-03	0.827	0.723	NK cells	pre
IL2RB	ENSG00000100385	0.355208	1.16e-06	2.15e-02	0.347	0.2	NK cells	pre
RPL41	ENSG00000229117	0.351875	1.10e-21	2.03e-17	1	1	NK cells	pre
IFITM1	ENSG00000185885	0.349942	2.75e-07	5.09e-03	0.413	0.255	NK cells	pre
RPL23	ENSG00000125691	0.342229	9.53e-11	1.76e-06	0.991	0.98	NK cells	pre
EIF5A	ENSG00000288145	0.330288	1.09e-08	2.02e-04	0.427	0.234	NK cells	pre
MT-ND2	ENSG00000198763	0.317908	2.68e-11	4.96e-07	1	0.998	NK cells	pre
CD44	ENSG00000026508	0.299992	1.74e-08	3.22e-04	0.489	0.277	NK cells	pre
RPL31	ENSG00000071082	0.298289	2.51e-10	4.64e-06	1	1	NK cells	pre
S100A8	ENSG00000143546	0.288125	1.63e-07	3.02e-03	0.449	0.264	NK cells	pre
RPS24	ENSG00000138326	0.279524	3.20e-10	5.92e-06	1	0.998	NK cells	pre
FXYD5	ENSG00000089327	0.27064	1.35e-06	2.49e-02	0.631	0.442	NK cells	pre
RPL35A	ENSG00000182899	0.261778	3.29e-09	6.09e-05	0.996	1	NK cells	pre
RPS19	ENSG00000105372	0.25707	2.36e-08	4.36e-04	1	1	NK cells	pre
EMP3	ENSG00000142227	-0.362687	6.95e-07	1.29e-02	0.662	0.766	NK cells	pre
GIMAP7	ENSG00000179144	-0.370117	1.05e-08	1.95e-04	0.267	0.489	NK cells	pre
ANXA1	ENSG00000135046	-0.39027	1.15e-07	2.12e-03	0.422	0.625	NK cells	pre
SUB1	ENSG00000113387	-0.424887	2.38e-08	4.39e-04	0.649	0.766	NK cells	pre
GZMH	ENSG00000100450	-0.503043	1.95e-09	3.60e-05	0.547	0.738	NK cells	pre
GZMA	ENSG00000145649	-0.514777	8.00e-12	1.48e-07	0.809	0.941	NK cells	pre
FGFBP2	ENSG00000137441	-0.550693	2.80e-12	5.18e-08	0.271	0.54	NK cells	pre
LGALS1	ENSG00000100097	-0.578071	5.13e-07	9.48e-03	0.6	0.74	NK cells	pre
CCL5	ENSG00000274233	-0.617981	1.01e-15	1.86e-11	0.827	0.936	NK cells	pre
IFI6	ENSG00000126709	0.844363	0.00e+00	0.00e+00	0.551	0.352	Malignant cells	pre
ANKRD28	ENSG00000206560	0.815207	0.00e+00	0.00e+00	0.48	0.287	Malignant cells	pre
ISG15	ENSG00000187608	0.771683	0.00e+00	0.00e+00	0.535	0.373	Malignant cells	pre
RPS29	ENSG00000213741	0.749428	0.00e+00	0.00e+00	1	0.997	Malignant cells	pre
CD99	ENSG00000002586	0.739337	0.00e+00	0.00e+00	0.544	0.377	Malignant cells	pre
RP11-620J15.3	NA	0.736126	0.00e+00	0.00e+00	0.387	0.043	Malignant cells	pre
RPS21	ENSG00000171858	0.726499	0.00e+00	0.00e+00	0.993	0.955	Malignant cells	pre
MGST1	ENSG00000008394	0.700026	0.00e+00	0.00e+00	0.506	0.273	Malignant cells	pre
HINT1	ENSG00000169567	0.68751	0.00e+00	0.00e+00	0.729	0.699	Malignant cells	pre
RPS3	ENSG00000149273	0.649272	0.00e+00	0.00e+00	0.997	0.998	Malignant cells	pre
SERPINB1	ENSG00000021355	0.640085	0.00e+00	0.00e+00	0.627	0.439	Malignant cells	pre
RPL31	ENSG00000071082	0.625954	0.00e+00	0.00e+00	0.995	0.985	Malignant 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
FAM65B	NA	0.533292	1.37e-25	2.54e-21	0.553	0.308	cDCs	post
PLAC8	ENSG00000145287	0.528587	2.21e-21	4.09e-17	0.456	0.225	cDCs	post
PPBP	ENSG00000163736	0.505803	2.08e-20	3.85e-16	0.333	0.117	cDCs	post
CST3	ENSG00000101439	0.480046	1.81e-14	3.35e-10	1	1	cDCs	post
DDX5	ENSG00000108654	0.472657	1.56e-24	2.89e-20	0.909	0.857	cDCs	post
IFI16	ENSG00000163565	0.438091	1.43e-20	2.64e-16	0.608	0.404	cDCs	post
TMSB4X	ENSG00000205542	0.429935	1.68e-44	3.07e-40	1	1	cDCs	post
OFD1	ENSG00000046651	0.425462	3.67e-20	6.78e-16	0.364	0.151	cDCs	post
MT-ND5	ENSG00000198786	0.421819	3.28e-20	6.06e-16	0.962	0.938	cDCs	post
PNRC1	ENSG00000146278	0.413966	2.08e-19	3.84e-15	0.729	0.538	cDCs	post
IFI6	ENSG00000126709	0.39485	2.75e-13	5.08e-09	0.346	0.18	cDCs	post
MARCKS	ENSG00000277443	0.390306	4.53e-16	8.37e-12	0.383	0.193	cDCs	post
DUSP1	ENSG00000120129	0.38905	1.78e-15	3.30e-11	0.869	0.824	cDCs	post
UBC	ENSG00000150991	0.38515	3.08e-16	5.69e-12	0.909	0.852	cDCs	post
ISG15	ENSG00000187608	0.377621	1.25e-08	2.31e-04	0.388	0.251	cDCs	post
NKG7	ENSG00000105374	0.374803	2.28e-14	4.22e-10	0.351	0.171	cDCs	post
TPM3	ENSG00000143549	0.371497	1.24e-13	2.29e-09	0.847	0.777	cDCs	post
PSAP	ENSG00000197746	0.368768	1.41e-14	2.61e-10	0.809	0.721	cDCs	post
ITGA4	ENSG00000115232	0.357326	2.23e-16	4.13e-12	0.421	0.225	cDCs	post
CALM2	ENSG00000143933	0.351482	8.02e-12	1.48e-07	0.927	0.904	cDCs	post
CKLF	ENSG00000217555	0.326515	8.97e-08	1.66e-03	0.646	0.579	cDCs	post
MEF2C	ENSG00000081189	0.326301	1.20e-12	2.22e-08	0.668	0.521	cDCs	post
MYL12A	ENSG00000101608	0.318112	1.99e-14	3.67e-10	0.959	0.934	cDCs	post
ZFAS1	ENSG00000177410	0.3178	4.50e-12	8.31e-08	0.766	0.622	cDCs	post
N4BP2L2	ENSG00000244754	0.314094	2.91e-13	5.38e-09	0.526	0.348	cDCs	post
RNASET2	ENSG00000026297	0.31317	3.28e-12	6.07e-08	0.748	0.626	cDCs	post
FTL	ENSG00000087086	0.30647	1.85e-06	3.42e-02	1	1	cDCs	post
HLA-DPA1	ENSG00000228163	0.305883	2.12e-15	3.92e-11	0.994	1	cDCs	post
MORF4L1	ENSG00000185787	0.305408	7.90e-11	1.46e-06	0.636	0.496	cDCs	post
DHRS9	ENSG00000073737	0.299966	5.37e-19	9.92e-15	0.254	0.074	cDCs	post
FOS	ENSG00000170345	0.299254	1.17e-08	2.16e-04	0.968	0.974	cDCs	post
PTPRC	ENSG00000262418	0.298734	7.35e-10	1.36e-05	0.781	0.718	cDCs	post
PKIB	ENSG00000135549	0.294745	2.64e-14	4.88e-10	0.305	0.136	cDCs	post
NCF1	ENSG00000158517	0.294525	8.95e-11	1.65e-06	0.349	0.196	cDCs	post
RPS19	ENSG00000105372	0.292499	5.01e-30	9.26e-26	1	1	cDCs	post
HLA-A	ENSG00000227715	0.289387	8.65e-09	1.60e-04	0.877	0.834	cDCs	post
DUSP6	ENSG00000139318	0.286079	2.61e-12	4.82e-08	0.254	0.106	cDCs	post
CCL5	ENSG00000274233	0.284856	2.31e-06	4.28e-02	0.254	0.153	cDCs	post
RP11-386I14.4	NA	0.284473	1.90e-07	3.52e-03	0.373	0.257	cDCs	post
B2M	ENSG00000273686	0.28138	3.06e-26	5.66e-22	1	1	cDCs	post
SEPT7	NA	0.280877	1.33e-09	2.46e-05	0.614	0.478	cDCs	post
NPM1	ENSG00000181163	0.279749	2.53e-07	4.68e-03	0.777	0.775	cDCs	post
C12orf57	ENSG00000111678	0.276805	5.43e-08	1.00e-03	0.378	0.251	cDCs	post
EMB	ENSG00000170571	0.272402	7.56e-10	1.40e-05	0.359	0.219	cDCs	post
RPL36AL	ENSG00000165502	0.265482	2.41e-11	4.46e-07	0.876	0.858	cDCs	post
LCP1	ENSG00000136167	0.259586	4.33e-08	8.01e-04	0.738	0.63	cDCs	post
LST1	ENSG00000235915	0.255836	3.58e-08	6.62e-04	0.954	0.935	cDCs	post
SH3BGRL	ENSG00000131171	0.254112	3.31e-08	6.13e-04	0.633	0.513	cDCs	post
CAPG	ENSG00000042493	-0.250176	3.65e-13	6.75e-09	0.396	0.607	cDCs	post
PLD4	ENSG00000166428	-0.250526	6.92e-14	1.28e-09	0.179	0.364	cDCs	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 5 known drug-resistant mechanisms in malignant cells

Mechnism	Pval	FDR	Signature	Geneset	Overlap	Background	Cell type	Enriched Genes
Unusual Activation of Pro-survival Pathway	8.40e-09	4.20e-08	239	781	28	23467	Malignant cells	ANXA2,CDK6,GSTP1,ISG15,JUN,MCL1,MAP1LC3B,RPS6,S100A4,SOX4,HSPA5,BTG1,CD44,CLU,CXCR4,DUSP1,EGR1,GAPDH,NFKBIA,IL1B,MAP3K8,RAC1,HNRNPA1,S100A8,S100A11,SOD2,TNFAIP3,NPM1
Drug Inactivation by Structure Modification	3.10e-02	7.70e-02	239	27	2	23467	Malignant cells	GSTP1,SOD2
Aberration of the Drug's Therapeutic Target	6.40e-02	1.10e-01	239	90	3	23467	Malignant cells	CDK6,IL1B,NPM1
Epigenetic Alteration of DNA, RNA or Protein	4.90e-01	6.20e-01	239	455	5	23467	Malignant cells	LMNA,CXCR4,GAPDH,MAP3K8,TIMP1
Irregularity in Drug Uptake and Drug Efflux	1.00e+00	1.00e+00	239	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	14	186	0	23467	B cells	NA
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	31	186	0	23467	CD4+ T cells	NA
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	40	186	0	23467	CD8+ T cells	NA
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	29	186	0	23467	cDCs	NA
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	20	186	0	23467	Erythrocytes	NA
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	38	186	0	23467	NK 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 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	1.10e-05	5.50e-05	120	781	15	23467	Malignant cells	ANXA2,DUSP6,ISG15,JUN,MCL1,RPS6,S100A4,CLU,NFKBIA,IL1B,S100A11,SOD2,TPT1,NPM1,CEBPD
Aberration of the Drug's Therapeutic Target	7.80e-02	1.90e-01	120	90	2	23467	Malignant cells	IL1B,NPM1
Drug Inactivation by Structure Modification	1.30e-01	2.20e-01	120	27	1	23467	Malignant cells	SOD2
Epigenetic Alteration of DNA, RNA or Protein	1.00e+00	1.00e+00	120	455	0	23467	Malignant cells
Irregularity in Drug Uptake and Drug Efflux	1.00e+00	1.00e+00	120	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	5.00e-01	5.00e-01	87	186	1	23467	CD4+ T cells	CXCR4
Regulation by the Disease Microenvironment	2.60e-01	2.60e-01	38	186	1	23467	CD8+ T cells	MALAT1
Regulation by the Disease Microenvironment	7.20e-02	7.20e-02	197	186	4	23467	cDCs	CXCR4,IL1B,VIM,MALAT1
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	86	186	0	23467	Erythrocytes	NA
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	23	186	0	23467	NK cells	NA
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	10	186	0	23467	pDCs	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

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 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__M05939	7.63	0.238	ZNF471 (directAnnotation).	B cells
	transfac_pro__M06665	6.65	0.209	ZNF599 (directAnnotation).	B cells
	transfac_pro__M06192	6.16	0.195	ZNF135 (directAnnotation).	B cells
	transfac_pro__M05907	5.53	0.177	ZNF416 (directAnnotation).	B cells
	transfac_pro__M06969	5.45	0.175	EBF4 (inferredBy_Orthology).	B cells
	metacluster_106.2	5.36	0.172	ZBTB32 (directAnnotation).	B cells
	taipale_tf_pairs__HOXB2_ETV7_TAATKNNNNGNNNNNNCTTCCNN_CAP_repr	5.33	0.171	ETV7; HOXB2 (directAnnotation).	B cells
	transfac_pro__M05624	4.95	0.16	ZSCAN9 (directAnnotation).	B cells
	transfac_pro__M04906	4.88	0.158	SIN3A (directAnnotation).	B cells
	transfac_pro__M04706	4.84	0.157	RELA (directAnnotation).	B 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__GCM1_MAX_NNCACGTGNNNNNNNNNNRTGCGGGYRN_CAP_repr	12.7	0.988	GCM1; MAX (directAnnotation).	B cells
	tfdimers__MD00031	12.7	0.982	MYB; ZEB1 (directAnnotation).	B cells
	transfac_pro__M06362	12.6	0.977	ZNF730 (directAnnotation).	B cells
	transfac_pro__M06490	12.6	0.976	ZNF664 (directAnnotation).	B cells
	taipale__NR4A2_full_AGGTCANNNNNTGACCT_repr	12.5	0.969	NR4A2 (directAnnotation).	B cells
	dbtfbs__CHAMP1_K562_ENCSR065XVO_merged_N1	12.4	0.964	CHAMP1 (directAnnotation).	B cells
	taipale_tf_pairs__GCM1_MAX_NNCACGTGNNNNNNNNNNRTGCGGGYRN_CAP	12.3	0.955	GCM1; MAX (directAnnotation).	B cells
	hocomoco__HSFY1_HUMAN.H11MO.0.D	12.1	0.938	HSFY1; HSFY2 (directAnnotation).	B cells
	cisbp__M00808	12.1	0.937	MYPOP (inferredBy_Orthology).	B cells
	tfdimers__MD00115	11.9	0.925	E2F1; NR1I2; RXRA (directAnnotation).	B 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_22.13	5.1	0.117	MAFK (inferredBy_Orthology).	CD4+ T cells
	metacluster_22.36	4.98	0.115	BACH2 (directAnnotation).	CD4+ T cells
	kznf__ZNF485_Imbeault2017_RP_RCADE	4.93	0.114	ZNF485 (directAnnotation).	CD4+ T cells
	metacluster_22.37	4.79	0.111	BACH1 (directAnnotation).	CD4+ T cells
	transfac_pro__M06849	4.7	0.109	ZNF528 (directAnnotation).	CD4+ T cells
	metacluster_22.19	4.66	0.109	NFE2 (directAnnotation).	CD4+ T cells
	transfac_pro__M01229	4.56	0.107	GTF2IRD1 (directAnnotation).	CD4+ T cells
	metacluster_22.34	4.54	0.106	BACH2 (directAnnotation).	CD4+ T cells
	transfac_pro__M05636	4.54	0.106	ZNF134; ZNF154; ZNF256; ZNF304; ZNF418; ZNF419; ZNF480; ZNF548; ZNF549; ZNF552; ZNF561; ZNF562; ZNF584; ZNF586; ZNF587B; ZNF610; ZNF772; ZNF773; ZNF792; ZNF793; ZNF837 (inferredBy_Orthology).	CD4+ T cells
	metacluster_84.7	4.53	0.106	RARA (directAnnotation).	CD4+ T cells

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

motif	motif	NES	AUC	TF_highConf	Cell_type
	taipale_tf_pairs__ERF_HOXA3_RSCGGAWNNNNNNNYMATTA_CAP_repr	6.53	0.124	ERF; HOXA3 (directAnnotation).	CD4+ T cells
	jaspar__MA0604.1	6.14	0.117	ATF1 (inferredBy_Orthology).	CD4+ T cells
	transfac_pro__M05894	5.42	0.105	ZNF565 (directAnnotation).	CD4+ T cells
	taipale_tf_pairs__ETV2_HOXA2_NCCGGAAGNNNNNNYMATTA_CAP	5.31	0.103	ETV2; HOXA2 (directAnnotation).	CD4+ T cells
	transfac_pro__M06317	5.31	0.103	ZNF829 (directAnnotation).	CD4+ T cells
	taipale_cyt_meth__ZNF385D_NCGTCGCGACGN_eDBD_repr	4.97	0.0976	ZNF385D (directAnnotation).	CD4+ T cells
	transfac_pro__M06569	4.89	0.0961	ZNF775 (directAnnotation).	CD4+ T cells
	taipale_tf_pairs__ELF2_NATGCGGAAGTR_HT	4.79	0.0945	ELF2 (directAnnotation).	CD4+ T cells
	cisbp__M01725	4.57	0.0908	SREBF2 (inferredBy_Orthology).	CD4+ T cells
	jaspar__MA1509.1	4.28	0.086	IRF6 (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
FOS	tfdimers__MD00090	up	CD4+ T cells	post
FOS	metacluster_50.1	up	CD4+ T cells	post
FOS	metacluster_137.2	up	CD4+ T cells	post
FOS	metacluster_157.2	up	cDCs	post
JUN	metacluster_157.2	up	cDCs	post
JUNB	metacluster_157.2	down	cDCs	post
CEBPD	taipale_tf_pairs__FLI1_CEBPD_RNCGGANNTTGCGCAAN_CAP	down	cDCs	post
IRF1	tfdimers__MD00527	down	cDCs	post
FOS	tfdimers__MD00475	up	Erythrocytes	post
FOS	tfdimers__MD00141	up	Erythrocytes	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."