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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: GSE169246_PacTissue

Dataset summary for GSE169246_PacTissue

Datast information	Dataset	GSE169246_PacTissue
	PMID	34653365
	Raw data ID/link	NA
	Organism	Homo sapiens
	Source	patients
	Tissue	Tumor tissue
	Cancer type level1	Breast cancer
	Cancer type level2	Advanced triple-negative breast cancer (TNBC)
	Regimen	paclitaxel
	Drug type	Chemotherapy
	Sample size	pre (resistant 3, sensitive 3); post (resistant 4, sensitive 3)
	Cell number	67140
	Extract protocol	10x genomics
	Data processing	CellRanger 3.0.0
	Public date	Public on Sep 15, 2021
	Description	This dataset has 7 patients, 6 of whom have both pre -and post-treatment samples.

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Drug summary for GSE169246_PacTissue

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"Paclitaxel"	DB01229	small molecule	TUBB1; BCL2; MAP4; MAP2; MAPT; NR1I2	Q9H4B7; P10415; P27816; P11137; P10636; O75469

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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
IGHG2	ENSG00000274497	2.7816	0.00e+00	0.00e+00	0.327	0.103	Plasma cells	pre
RPS27	ENSG00000177954	1.76376	0.00e+00	0.00e+00	0.904	0.515	Plasma cells	pre
RPS29	ENSG00000213741	1.69943	0.00e+00	0.00e+00	0.779	0.183	Plasma cells	pre
RPL39	ENSG00000198918	1.57149	0.00e+00	0.00e+00	0.859	0.442	Plasma cells	pre
TMSB10	ENSG00000034510	1.42431	0.00e+00	0.00e+00	0.678	0.256	Plasma cells	pre
RPL37	ENSG00000145592	1.40337	0.00e+00	0.00e+00	0.868	0.467	Plasma cells	pre
DNAJB1	ENSG00000132002	1.38838	0.00e+00	0.00e+00	0.658	0.289	Plasma cells	pre
RPS21	ENSG00000171858	1.36956	0.00e+00	0.00e+00	0.781	0.269	Plasma cells	pre
RPS28	ENSG00000233927	1.29402	0.00e+00	0.00e+00	0.941	0.673	Plasma cells	pre
HSP90AB1	ENSG00000096384	1.28558	0.00e+00	0.00e+00	0.627	0.334	Plasma cells	pre
RPLP2	ENSG00000177600	1.27729	0.00e+00	0.00e+00	0.819	0.434	Plasma cells	pre
TMSB4X	ENSG00000205542	1.25626	0.00e+00	0.00e+00	0.638	0.338	Plasma cells	pre
RPL34	ENSG00000109475	1.25316	0.00e+00	0.00e+00	0.855	0.551	Plasma cells	pre
FTH1	ENSG00000167996	1.25267	0.00e+00	0.00e+00	0.75	0.449	Plasma cells	pre
HSP90AA1	ENSG00000080824	1.24079	0.00e+00	0.00e+00	0.722	0.511	Plasma cells	pre
RPL30	ENSG00000156482	1.23595	0.00e+00	0.00e+00	0.846	0.528	Plasma cells	pre
IGHG4	ENSG00000277016	1.18467	9.00e-07	1.84e-02	0.346	0.269	Plasma cells	pre
RPL36	ENSG00000130255	1.18361	0.00e+00	0.00e+00	0.803	0.427	Plasma cells	pre
PTMA	ENSG00000187514	1.18166	0.00e+00	0.00e+00	0.738	0.368	Plasma cells	pre
RPS12	ENSG00000112306	1.16936	0.00e+00	0.00e+00	0.899	0.695	Plasma cells	pre
RPS15A	ENSG00000134419	1.16874	0.00e+00	0.00e+00	0.904	0.7	Plasma cells	pre
RPL26	ENSG00000161970	1.15238	0.00e+00	0.00e+00	0.836	0.561	Plasma cells	pre
RPL37A	ENSG00000197756	1.13982	0.00e+00	0.00e+00	0.789	0.393	Plasma cells	pre
PFN1	ENSG00000108518	1.13571	0.00e+00	0.00e+00	0.501	0.152	Plasma cells	pre
RPL17	ENSG00000265681	1.13377	0.00e+00	0.00e+00	0.774	0.457	Plasma cells	pre
RPS27A	ENSG00000143947	1.12828	0.00e+00	0.00e+00	0.848	0.629	Plasma cells	pre
RPS24	ENSG00000138326	1.12054	0.00e+00	0.00e+00	0.803	0.526	Plasma cells	pre
HSPA8	ENSG00000109971	1.11782	0.00e+00	0.00e+00	0.664	0.408	Plasma cells	pre
UBB	ENSG00000170315	1.1174	0.00e+00	0.00e+00	0.7	0.42	Plasma cells	pre
RPL32	ENSG00000144713	1.10471	0.00e+00	0.00e+00	0.882	0.655	Plasma cells	pre
BTG1	ENSG00000133639	1.09897	0.00e+00	0.00e+00	0.488	0.16	Plasma cells	pre
RPS25	ENSG00000280831	1.09824	0.00e+00	0.00e+00	0.796	0.487	Plasma cells	pre
HSPH1	ENSG00000120694	1.08128	0.00e+00	0.00e+00	0.462	0.118	Plasma cells	pre
RPS3A	ENSG00000145425	1.06705	0.00e+00	0.00e+00	0.84	0.627	Plasma cells	pre
JUNB	ENSG00000171223	1.06694	0.00e+00	0.00e+00	0.586	0.221	Plasma cells	pre
RPS18	ENSG00000223367	1.06233	0.00e+00	0.00e+00	0.904	0.75	Plasma cells	pre
PNRC1	ENSG00000146278	1.05859	0.00e+00	0.00e+00	0.483	0.13	Plasma cells	pre
RPS23	ENSG00000186468	1.0578	0.00e+00	0.00e+00	0.824	0.563	Plasma cells	pre
HSPE1	ENSG00000115541	1.04983	0.00e+00	0.00e+00	0.608	0.22	Plasma cells	pre
RPL12	ENSG00000197958	1.04929	0.00e+00	0.00e+00	0.775	0.526	Plasma cells	pre
RPS7	ENSG00000171863	1.03677	0.00e+00	0.00e+00	0.809	0.572	Plasma cells	pre
HSPD1	ENSG00000144381	1.0295	0.00e+00	0.00e+00	0.508	0.172	Plasma cells	pre
RPL13A	ENSG00000142541	1.02517	0.00e+00	0.00e+00	0.601	0.246	Plasma cells	pre
RPL28	ENSG00000108107	1.01727	0.00e+00	0.00e+00	0.89	0.757	Plasma cells	pre
RPL35A	ENSG00000182899	1.01697	0.00e+00	0.00e+00	0.839	0.572	Plasma cells	pre
RPL13	ENSG00000167526	1.01665	0.00e+00	0.00e+00	0.931	0.827	Plasma cells	pre
RPS2	ENSG00000140988	1.00411	0.00e+00	0.00e+00	0.795	0.632	Plasma cells	pre
HLA-A	ENSG00000227715	0.990731	0.00e+00	0.00e+00	0.651	0.354	Plasma cells	pre
IL32	ENSG00000008517	0.986918	0.00e+00	0.00e+00	0.398	0.072	Plasma cells	pre
RPS6	ENSG00000137154	0.982616	0.00e+00	0.00e+00	0.792	0.609	Plasma 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
CD37	ENSG00000104894	-0.305656	6.19e-14	1.27e-09	0.969	0.992	B cells	post
VPS37B	ENSG00000139722	-0.308771	1.40e-08	2.86e-04	0.346	0.488	B cells	post
RPL29	ENSG00000162244	-0.310326	4.22e-22	8.63e-18	0.998	0.997	B cells	post
FAU	ENSG00000149806	-0.311374	7.07e-29	1.45e-24	0.997	0.997	B cells	post
CD79A	ENSG00000105369	-0.311733	4.78e-13	9.77e-09	0.95	0.975	B cells	post
MT-CO2	ENSG00000198712	-0.316306	1.96e-25	4.01e-21	0.998	1	B cells	post
LYN	ENSG00000254087	-0.317721	2.86e-09	5.85e-05	0.437	0.565	B cells	post
HLA-DRB1	ENSG00000228080	-0.319345	1.03e-17	2.11e-13	0.985	0.989	B cells	post
RPL10	ENSG00000147403	-0.32025	8.39e-29	1.72e-24	0.999	1	B cells	post
SMDT1	ENSG00000274112	-0.325399	8.30e-16	1.70e-11	0.377	0.584	B cells	post
MT-ND4L	ENSG00000212907	-0.328716	9.88e-24	2.02e-19	0.992	1	B cells	post
MYADM	ENSG00000179820	-0.332225	3.26e-14	6.66e-10	0.268	0.474	B cells	post
RASGEF1B	ENSG00000138670	-0.333666	1.71e-06	3.50e-02	0.366	0.476	B cells	post
RPL11	ENSG00000142676	-0.336306	5.28e-29	1.08e-24	0.999	0.997	B cells	post
ITM2B	ENSG00000136156	-0.337294	4.92e-14	1.01e-09	0.388	0.579	B cells	post
RPL35A	ENSG00000182899	-0.337756	6.78e-28	1.39e-23	0.996	0.994	B cells	post
TUBA1A	ENSG00000167552	-0.340243	5.45e-08	1.11e-03	0.508	0.645	B cells	post
RPS8	ENSG00000142937	-0.351089	4.86e-35	9.93e-31	0.999	1	B cells	post
HLA-DRB5	ENSG00000198502	-0.35355	3.94e-09	8.05e-05	0.765	0.806	B cells	post
PDE4B	ENSG00000184588	-0.358245	2.22e-11	4.55e-07	0.384	0.557	B cells	post
RPS13	ENSG00000110700	-0.360462	9.69e-33	1.98e-28	0.997	0.997	B cells	post
CREM	ENSG00000095794	-0.365153	1.90e-09	3.89e-05	0.445	0.601	B cells	post
MT-CO1	ENSG00000198804	-0.36614	5.08e-23	1.04e-18	0.997	1	B cells	post
MT-CYB	ENSG00000198727	-0.37601	1.57e-24	3.21e-20	0.993	1	B cells	post
BIRC3	ENSG00000023445	-0.377627	6.54e-13	1.34e-08	0.431	0.615	B cells	post
RPL39	ENSG00000198918	-0.382754	1.74e-31	3.57e-27	0.996	1	B cells	post
RPS24	ENSG00000138326	-0.397331	4.34e-30	8.87e-26	0.998	0.997	B cells	post
CCL4	ENSG00000277943	-0.402052	2.77e-26	5.67e-22	0.077	0.271	B cells	post
CD74	ENSG00000019582	-0.402619	1.40e-45	4.09e-41	0.999	1	B cells	post
RPL34	ENSG00000109475	-0.406797	2.04e-37	4.17e-33	0.999	0.997	B cells	post
EMP3	ENSG00000142227	-0.409698	4.06e-11	8.30e-07	0.433	0.596	B cells	post
SELL	ENSG00000188404	-0.411394	4.19e-17	8.57e-13	0.423	0.629	B cells	post
PLPP5	ENSG00000147535	-0.41976	4.63e-22	9.47e-18	0.162	0.374	B cells	post
SMAP2	ENSG00000084070	-0.432877	1.11e-15	2.27e-11	0.482	0.662	B cells	post
EZR	ENSG00000092820	-0.464248	2.68e-19	5.48e-15	0.692	0.839	B cells	post
TAGLN2	ENSG00000158710	-0.561754	7.03e-23	1.44e-18	0.716	0.856	B cells	post
RUBCNL	ENSG00000102445	-0.584493	1.35e-31	2.76e-27	0.26	0.537	B cells	post
FTH1	ENSG00000167996	-0.588589	1.06e-14	2.18e-10	0.995	1	B cells	post
HERPUD1	ENSG00000051108	-0.605185	3.43e-18	7.02e-14	0.704	0.817	B cells	post
YBX3	ENSG00000060138	-0.724281	2.13e-40	4.35e-36	0.141	0.429	B cells	post
MT-ND3	ENSG00000198840	-0.735088	0.00e+00	0.00e+00	0.984	0.997	B cells	post
CD55	ENSG00000196352	-0.739565	3.24e-27	6.63e-23	0.576	0.762	B cells	post
ZFP36L2	ENSG00000152518	-0.955523	4.26e-43	8.72e-39	0.587	0.842	B 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	5.60e-03	5.60e-03	410	186	9	23467	B cells	BCL2,BRAF,NFKB1,TGFBR2,ZEB2,CXCR4,RHOB,VIM,MALAT1
Regulation by the Disease Microenvironment	1.20e-01	1.20e-01	240	186	4	23467	CD4+ T cells	NFKB1,HNRNPA2B1,LDHB,MALAT1
Regulation by the Disease Microenvironment	1.20e-01	1.20e-01	329	186	5	23467	CD8+ T cells	BRAF,NFKB1,HNRNPA2B1,MALAT1,TSPYL2
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	52	186	0	23467	cDCs	NA
Regulation by the Disease Microenvironment	5.90e-03	5.90e-03	270	186	7	23467	Mono_Macro	MMP9,CXCR4,IL1B,VIM,MALAT1,FBP1,TIMP2
Regulation by the Disease Microenvironment	2.80e-01	2.80e-01	41	186	1	23467	NK cells	TGFB1
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	9	186	0	23467	pDCs	NA
Regulation by the Disease Microenvironment	1.40e-01	1.40e-01	254	186	4	23467	Plasma cells	CXCR4,HNRNPA2B1,VIM,MALAT1

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	7.70e-01	7.70e-01	186	186	1	23467	B cells	HNRNPA2B1
Regulation by the Disease Microenvironment	5.10e-02	5.10e-02	105	186	3	23467	CD4+ T cells	TGFB1,VIM,TSPYL2
Regulation by the Disease Microenvironment	2.60e-01	2.60e-01	124	186	2	23467	CD8+ T cells	CXCR4,TSPYL2
Regulation by the Disease Microenvironment	1.60e-01	1.60e-01	175	186	3	23467	cDCs	SNAI1,VIM,FBP1
Regulation by the Disease Microenvironment	1.00e-01	1.00e-01	224	186	4	23467	Mono_Macro	NFKB1,SNAI1,VIM,FBP1
Regulation by the Disease Microenvironment	3.60e-02	3.60e-02	228	186	5	23467	NK cells	CXCR4,HNRNPA2B1,STAT3,VIM,TSPYL2
Regulation by the Disease Microenvironment	1.50e-02	1.50e-02	24	186	2	23467	pDCs	VIM,MALAT1
Regulation by the Disease Microenvironment	4.60e-01	4.60e-01	77	186	1	23467	Plasma cells	VIM

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
	cisbp__M00775	3.6	0.124	ZBTB1 (inferredBy_Orthology).	B cells
	transfac_pro__M00514	3.53	0.122	ATF4 (directAnnotation).	B cells
	metacluster_126.2	3.48	0.121	ZBTB4; ZBTB4 (directAnnotation).	B cells
	metacluster_67.2	3.44	0.12	ZNF501 (directAnnotation). ACAA1; E2F2; E2F2; E2F3; E2F3; FOXN4 (inferredBy_Orthology).	B cells
	taipale_tf_pairs__ETV5_HES7_CCGGAANNNNNNCACGTG_CAP	3.36	0.118	ETV5; HES7 (directAnnotation).	B cells
	taipale_cyt_meth__ZNF460_NRMCGCCCCCCGN_eDBD_meth	3.36	0.118	ZNF460 (directAnnotation).	B cells
	metacluster_3.10	3.32	0.117	KLF2; KLF4 (directAnnotation).	B cells
	transfac_pro__M07436	3.31	0.117	WT1 (directAnnotation).	B cells
	cisbp__M00249	3.3	0.117	WT1 (directAnnotation).	B cells
	taipale_cyt_meth__E2F2_NCGCGCGCGCM_eDBD_meth	3.3	0.117	E2F2 (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
	hdpi__FLI1	7.1	0.0886	FLI1 (directAnnotation).	B cells
	metacluster_2.8	5.67	0.0748	IRF4; IRF5; IRF6; IRF9 (directAnnotation). IRF3; IRF5; IRF5; IRF6 (inferredBy_Orthology).	B cells
	taipale_tf_pairs__ETS2_RCCGGAAGTG_HT	5.56	0.0737	ETS2 (directAnnotation).	B cells
	taipale_tf_pairs__TEAD4_ETV1_RSCGGAAATRCM_CAP	4.67	0.0652	ETV1; TEAD4 (directAnnotation).	B cells
	tfdimers__MD00007	4.66	0.065	E2F1; IRF8 (directAnnotation).	B cells
	taipale_tf_pairs__ELF2_NATGCGGAAGTR_HT	4.57	0.0642	ELF2 (directAnnotation).	B cells
	taipale_tf_pairs__GCM1_ETV4_RTGCGGGCGGAAGTR_CAP	4.48	0.0634	ETV4; GCM1 (directAnnotation).	B cells
	jaspar__MA1708.1	4.4	0.0626	ETV7 (directAnnotation).	B cells
	transfac_pro__M06839	4.32	0.0618	ZNF263 (inferredBy_Orthology).	B cells
	taipale_tf_pairs__ELK1_HOXA1_RCCGGAAGTAATTA_HT	4.17	0.0604	ELK1; HOXA1 (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
	hocomoco__TYY2_HUMAN.H11MO.0.D	6.62	0.104	YY2 (directAnnotation).	B cells
	metacluster_141.2	6.22	0.0989	E2F2; E2F3 (directAnnotation).	B cells
	metacluster_21.4	5.73	0.0929	HSF1; HSF1; HSF2 (directAnnotation). HSF1; HSF2; HSF4; HSF5; HSFX1; HSFX2; HSFX3; HSFX4; HSFY1; HSFY2 (inferredBy_Orthology).	B cells
	metacluster_21.5	5.36	0.0882	HOXB2; HSF1; HSF1; HSF1; HSF1; HSF1; HSF1; HSF1; HSF1; HSF2; HSF2; HSF2; HSF2; HSF2; HSF2; HSF4; HSF4; HSF4 (directAnnotation). HSF1; HSF1; HSF1; HSF1; HSF1; HSF1; HSF1; HSF2; HSF2; HSF2; HSF2; HSF4; HSF4; HSF4; HSF4; HSF5; HSF5; HSF5; HSF5; HSFX1; HSFX1; HSFX1; HSFX1; HSFX2; HSFX2; HSFX2; HSFX2; HSFX3; HSFX3; HSFX3; HSFX3; HSFX4; HSFX4; HSFX4; HSFX4; HSFY1; HSFY1; HSFY1; HSFY1; HSFY2; HSFY2; HSFY2; HSFY2 (inferredBy_Orthology).	B cells
	metacluster_56.5	5.34	0.088	HSF1; HSF1; HSF2 (directAnnotation). HSF1; HSF2; HSF4; HSF5; HSFX1; HSFX2; HSFX3; HSFX4; HSFY1; HSFY2 (inferredBy_Orthology).	B cells
	flyfactorsurvey__pho_SOLEXA_F1-3	4.91	0.0826	YY1 (inferredBy_Orthology).	B cells
	metacluster_174.3	4.86	0.082	MBD2; NFYA; NFYB; NFYC; PBX3 (directAnnotation).	B cells
	swissregulon__hs__HSF2	4.86	0.082	HSF2 (directAnnotation).	B cells
	taipale__YY2_DBD_NNCCGCCATNW_repr	4.67	0.0797	YY2 (directAnnotation).	B cells
	metacluster_174.2	4.54	0.0781	CEBPZ; CEBPZ; DRAP1; FOS; FOXI1; FOXI1; HMGXB3; IRF3; NFYA; NFYA; NFYA; NFYA; NFYA; NFYA; NFYA; NFYA; NFYA; NFYB; NFYB; NFYB; NFYB; NFYB; NFYC; NFYC; NFYC; NFYC; NFYC; NFYC; NFYC; PBX3; PBX3; SP2 (directAnnotation). NFYA; NFYA; NFYC; PBX1; PBX3 (inferredBy_Orthology).	B 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
	metacluster_155.13	5.13	0.109	ZNF135 (directAnnotation).	B cells
	metacluster_140.1	4.69	0.102	BCL11B; BCL11B (directAnnotation).	B cells
	taipale_tf_pairs__TEAD4_SPDEF_RGAATGCGGATN_CAP	4.35	0.0961	SPDEF; TEAD4 (directAnnotation).	B cells
	taipale_tf_pairs__ETV2_SOX15_RSCGGAWNNNNNNNACAATRN_CAP_repr	4.3	0.0951	ETV2; SOX15 (directAnnotation).	B cells
	transfac_pro__M06433	4.29	0.0951	ZNF571 (directAnnotation).	B cells
	transfac_pro__M05545	4.25	0.0944	IKZF4 (inferredBy_Orthology).	B cells
	tfdimers__MD00542	3.98	0.0899	E2F1; EBF1 (directAnnotation).	B cells
	tfdimers__MD00016	3.92	0.0888	MYCN (directAnnotation).	B cells
	taipale_tf_pairs__HOXB2_HOXB13_NNATCATNGTAAA_CAP_repr	3.87	0.088	HOXB13; HOXB2 (directAnnotation).	B cells
	transfac_pro__M06073	3.84	0.0875	ZNF749 (directAnnotation).	B 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
BATF	metacluster_50.1	up	CD4+ T cells	post
JUN	metacluster_50.1	up	CD4+ T cells	post
JUNB	metacluster_50.1	up	CD4+ T cells	post
BATF	metacluster_157.2	up	CD4+ T cells	post
JUN	metacluster_157.2	up	CD4+ T cells	post
JUNB	metacluster_157.2	up	CD4+ T cells	post
JUN	tfdimers__MD00165	up	CD4+ T cells	post
JUNB	tfdimers__MD00165	up	CD4+ T cells	post
JUN	cisbp__M01816	up	CD4+ T cells	post
IRF7	metacluster_2.6	up	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."