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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_PacAteBlood

Dataset summary for GSE169246_PacAteBlood

Datast information	Dataset	GSE169246_PacAteBlood
	PMID	34653365
	Raw data ID/link	NA
	Organism	Homo sapiens
	Source	patients
	Tissue	Peripheral blood mononuclear cells
	Cancer type level1	Breast cancer
	Cancer type level2	Advanced triple-negative breast cancer (TNBC)
	Regimen	atezolizumab + paclitaxel
	Drug type	Immunotherapy
	Sample size	pre (resistant 7, sensitive 4); post (resistant 7, sensitive 4)
	Cell number	129562
	Extract protocol	10x genomics
	Data processing	CellRanger 3.0.0
	Public date	Public on Sep 15, 2021
	Description	This dataset has 11 patients with both pre -and post-treatment samples.

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Drug summary for GSE169246_PacAteBlood

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"Atezolizumab"	DB11595	biotech	CD274; PDCD1	Q9NZQ7; Q15116
"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
S100A4	ENSG00000196154	-0.32671	0.00e+00	0.00e+00	0.976	0.985	CD8+ T cells	pre
EMP3	ENSG00000142227	-0.337358	0.00e+00	0.00e+00	0.821	0.895	CD8+ T cells	pre
SH3BGRL3	ENSG00000142669	-0.341125	0.00e+00	0.00e+00	0.991	0.995	CD8+ T cells	pre
GNLY	ENSG00000115523	-0.343726	4.97e-28	9.63e-24	0.537	0.638	CD8+ T cells	pre
IFITM2	ENSG00000185201	-0.348285	0.00e+00	0.00e+00	0.873	0.904	CD8+ T cells	pre
CRIP1	ENSG00000213145	-0.431985	0.00e+00	0.00e+00	0.758	0.848	CD8+ T cells	pre
LGALS1	ENSG00000100097	-0.552713	0.00e+00	0.00e+00	0.435	0.612	CD8+ T cells	pre
RPS26	ENSG00000197728	0.794165	0.00e+00	0.00e+00	0.95	0.89	CD4+ T cells	pre
TXNIP	ENSG00000265972	0.487459	0.00e+00	0.00e+00	0.89	0.873	CD4+ T cells	pre
MT-ATP6	ENSG00000198899	0.406381	0.00e+00	0.00e+00	0.961	0.929	CD4+ T cells	pre
BTG1	ENSG00000133639	0.375733	0.00e+00	0.00e+00	0.815	0.761	CD4+ T cells	pre
MALAT1	ENSG00000251562	0.371474	0.00e+00	0.00e+00	1	1	CD4+ T cells	pre
CXCR4	ENSG00000121966	0.320772	0.00e+00	0.00e+00	0.292	0.155	CD4+ T cells	pre
ZFP36L2	ENSG00000152518	0.254483	2.60e-27	5.03e-23	0.573	0.496	CD4+ T cells	pre
ANXA1	ENSG00000135046	-0.253791	0.00e+00	5.61e-45	0.362	0.475	CD4+ T cells	pre
PCBP1	ENSG00000169564	-0.254211	1.90e-33	3.69e-29	0.46	0.519	CD4+ T cells	pre
S100A6	ENSG00000197956	-0.265486	0.00e+00	8.41e-45	0.794	0.873	CD4+ T cells	pre
CD74	ENSG00000019582	-0.279036	0.00e+00	0.00e+00	0.551	0.668	CD4+ T cells	pre
SH3BGRL3	ENSG00000142669	-0.285816	0.00e+00	0.00e+00	0.892	0.948	CD4+ T cells	pre
KLRB1	ENSG00000111796	-0.305821	0.00e+00	0.00e+00	0.15	0.25	CD4+ T cells	pre
LGALS1	ENSG00000100097	-0.423098	0.00e+00	0.00e+00	0.162	0.307	CD4+ T cells	pre
S100A4	ENSG00000196154	-0.464033	0.00e+00	0.00e+00	0.738	0.862	CD4+ T cells	pre
CRIP1	ENSG00000213145	-0.495314	0.00e+00	0.00e+00	0.627	0.792	CD4+ T cells	pre
RPS26	ENSG00000197728	0.905026	0.00e+00	0.00e+00	0.86	0.787	B cells	pre
TXNIP	ENSG00000265972	0.892811	0.00e+00	0.00e+00	0.862	0.745	B cells	pre
CXCR4	ENSG00000121966	0.727735	0.00e+00	0.00e+00	0.513	0.265	B cells	pre
BTG1	ENSG00000133639	0.716528	0.00e+00	0.00e+00	0.868	0.745	B cells	pre
TSC22D3	ENSG00000157514	0.542489	0.00e+00	0.00e+00	0.517	0.322	B cells	pre
MT-ND4L	ENSG00000212907	0.517877	0.00e+00	0.00e+00	0.99	0.956	B cells	pre
PTMA	ENSG00000187514	0.478132	0.00e+00	0.00e+00	0.989	0.951	B cells	pre
ZFP36L2	ENSG00000152518	0.399955	0.00e+00	0.00e+00	0.513	0.322	B cells	pre
H3F3B	NA	0.388163	0.00e+00	0.00e+00	0.754	0.628	B cells	pre
EEF1A1	ENSG00000156508	0.383827	0.00e+00	0.00e+00	1	1	B cells	pre
NPM1	ENSG00000181163	0.381564	0.00e+00	0.00e+00	0.708	0.494	B cells	pre
MT-ATP6	ENSG00000198899	0.374705	0.00e+00	0.00e+00	0.986	0.974	B cells	pre
RPL3	ENSG00000100316	0.366917	0.00e+00	0.00e+00	0.999	0.994	B cells	pre
SMAP2	ENSG00000084070	0.360286	0.00e+00	0.00e+00	0.43	0.225	B cells	pre
HNRNPA1	ENSG00000135486	0.359124	0.00e+00	0.00e+00	0.723	0.548	B cells	pre
HSP90AB1	ENSG00000096384	0.321246	0.00e+00	0.00e+00	0.674	0.485	B cells	pre
EEF1G	ENSG00000254772	0.316468	0.00e+00	0.00e+00	0.899	0.813	B cells	pre
YBX3	ENSG00000060138	0.312747	0.00e+00	0.00e+00	0.276	0.131	B cells	pre
RPL36A	ENSG00000241343	0.310788	0.00e+00	5.61e-45	0.808	0.696	B cells	pre
JCHAIN	ENSG00000132465	0.29301	7.66e-40	1.48e-35	0.361	0.231	B cells	pre
FAM129C	NA	0.275416	0.00e+00	0.00e+00	0.617	0.461	B cells	pre
ISG20	ENSG00000172183	0.269734	0.00e+00	4.74e-43	0.609	0.458	B cells	pre
EIF3E	ENSG00000104408	0.257667	0.00e+00	0.00e+00	0.581	0.397	B cells	pre
NCL	ENSG00000115053	0.254971	0.00e+00	0.00e+00	0.44	0.257	B cells	pre
HLA-A	ENSG00000227715	0.251605	0.00e+00	0.00e+00	0.971	0.928	B cells	pre
TMSB10	ENSG00000034510	-0.261871	0.00e+00	0.00e+00	1	1	B cells	pre
SH3BGRL3	ENSG00000142669	-0.286227	0.00e+00	0.00e+00	0.837	0.902	B 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
MT-ND4L	ENSG00000212907	-0.807838	7.21e-08	1.40e-03	0.853	0.887	Plasma cells	post
RPS29	ENSG00000213741	1.21644	1.32e-14	2.55e-10	0.949	0.736	pDCs	post
RPS21	ENSG00000171858	0.74582	3.32e-08	6.44e-04	0.975	0.954	pDCs	post
RPS28	ENSG00000233927	0.73364	2.16e-08	4.18e-04	0.987	0.977	pDCs	post
RPL41	ENSG00000229117	0.704997	5.18e-08	1.00e-03	0.962	0.885	pDCs	post
RPL39	ENSG00000198918	0.70171	7.64e-07	1.48e-02	0.962	0.931	pDCs	post
HLA-B	ENSG00000206450	0.697564	4.04e-09	7.83e-05	0.987	0.989	pDCs	post
RPS27	ENSG00000177954	0.696348	2.44e-06	4.72e-02	1	0.966	pDCs	post
CD4	ENSG00000010610	0.60179	2.34e-06	4.54e-02	0.797	0.517	pDCs	post
TYROBP	ENSG00000011600	0.569548	1.54e-06	2.99e-02	0.899	0.885	pDCs	post
S100A9	ENSG00000163220	-0.562496	6.80e-08	1.32e-03	0.076	0.46	pDCs	post
MT-CO2	ENSG00000198712	-0.600595	1.55e-07	3.01e-03	1	1	pDCs	post
MT-CO1	ENSG00000198804	-0.652543	4.25e-08	8.23e-04	1	1	pDCs	post
MT-CO3	ENSG00000198938	-0.67321	3.46e-08	6.69e-04	1	1	pDCs	post
ZFP36L2	ENSG00000152518	-0.701898	1.09e-07	2.11e-03	0.443	0.816	pDCs	post
MT-ATP8	ENSG00000228253	-0.71409	5.03e-07	9.75e-03	0.684	0.943	pDCs	post
LYZ	ENSG00000090382	-0.794495	4.67e-12	9.04e-08	0.076	0.609	pDCs	post
AHNAK	ENSG00000124942	-0.952898	2.49e-07	4.82e-03	0.342	0.701	pDCs	post
MT-ND4L	ENSG00000212907	-0.955449	4.97e-11	9.63e-07	0.873	1	pDCs	post
HBB	ENSG00000244734	-3.50683	4.82e-18	9.34e-14	0.025	0.69	pDCs	post
MYOM2	ENSG00000274137	0.776432	0.00e+00	0.00e+00	0.256	0.025	NK cells	post
HLA-B	ENSG00000206450	0.562509	0.00e+00	0.00e+00	0.999	0.997	NK cells	post
LINC00861	ENSG00000245164	0.497458	0.00e+00	0.00e+00	0.75	0.551	NK cells	post
MALAT1	ENSG00000251562	0.442838	0.00e+00	0.00e+00	1	1	NK cells	post
ALOX5AP	ENSG00000132965	0.397517	0.00e+00	0.00e+00	0.42	0.235	NK cells	post
KLRB1	ENSG00000111796	0.390928	0.00e+00	0.00e+00	0.719	0.576	NK cells	post
RPL37A	ENSG00000197756	0.372897	0.00e+00	0.00e+00	0.986	0.937	NK cells	post
CLIC3	ENSG00000169583	0.359869	0.00e+00	0.00e+00	0.665	0.591	NK cells	post
GZMA	ENSG00000145649	0.349664	0.00e+00	0.00e+00	0.896	0.886	NK cells	post
HLA-C	ENSG00000206435	0.349057	0.00e+00	0.00e+00	0.999	0.999	NK cells	post
MT-ND4	ENSG00000198886	0.348109	0.00e+00	0.00e+00	0.972	0.951	NK cells	post
EFHD2	ENSG00000142634	0.346943	0.00e+00	0.00e+00	0.666	0.557	NK cells	post
MT-ND3	ENSG00000198840	0.306624	0.00e+00	0.00e+00	0.997	0.982	NK cells	post
TRBC1	ENSG00000281981	0.306395	0.00e+00	4.45e-42	0.59	0.522	NK cells	post
RPS27	ENSG00000177954	0.304319	0.00e+00	0.00e+00	0.999	0.996	NK cells	post
RPL36A	ENSG00000241343	0.301591	0.00e+00	0.00e+00	0.624	0.469	NK cells	post
RPL38	ENSG00000172809	0.296826	0.00e+00	0.00e+00	0.934	0.795	NK cells	post
MYL12A	ENSG00000101608	0.279947	0.00e+00	0.00e+00	0.952	0.929	NK cells	post
CD3E	ENSG00000198851	0.279002	0.00e+00	0.00e+00	0.39	0.266	NK cells	post
RPS29	ENSG00000213741	0.264888	0.00e+00	0.00e+00	0.99	0.868	NK cells	post
TGFB1	ENSG00000105329	0.263808	0.00e+00	0.00e+00	0.545	0.431	NK cells	post
RPS21	ENSG00000171858	0.263435	0.00e+00	0.00e+00	0.991	0.932	NK cells	post
TMA7	ENSG00000232112	0.25721	0.00e+00	0.00e+00	0.868	0.778	NK cells	post
CD2	ENSG00000116824	0.251472	0.00e+00	2.27e-42	0.521	0.431	NK cells	post
RPL34	ENSG00000109475	0.251366	0.00e+00	0.00e+00	0.997	0.982	NK cells	post
ITGAX	ENSG00000140678	-0.250525	0.00e+00	0.00e+00	0.144	0.272	NK cells	post
SLC9A3R1	ENSG00000109062	-0.254281	0.00e+00	0.00e+00	0.561	0.66	NK cells	post
HIST1H1D	NA	-0.254639	0.00e+00	0.00e+00	0.153	0.283	NK cells	post
MT-CO3	ENSG00000198938	-0.260875	0.00e+00	0.00e+00	0.999	0.998	NK cells	post
HNRNPA2B1	ENSG00000122566	-0.262457	0.00e+00	0.00e+00	0.695	0.741	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	1.90e-01	1.90e-01	27	186	1	23467	B cells	CXCR4
Regulation by the Disease Microenvironment	7.00e-03	7.00e-03	16	186	2	23467	CD4+ T cells	CXCR4,MALAT1
Regulation by the Disease Microenvironment	5.60e-02	5.60e-02	48	186	2	23467	CD8+ T cells	CXCR4,MALAT1
Regulation by the Disease Microenvironment	5.30e-01	5.30e-01	222	186	2	23467	cDCs	HNRNPA2B1,VIM
Regulation by the Disease Microenvironment	1.60e-02	1.60e-02	186	186	5	23467	Mono_Macro	ZEB2,CX3CR1,CXCR4,VIM,MALAT1
Regulation by the Disease Microenvironment	2.70e-01	2.70e-01	40	186	1	23467	NK cells	CXCR4
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	8	186	0	23467	pDCs	NA
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	3	186	0	23467	Plasma cells	NA

Hallmark, KEGG and GOBP enrichment results for up-regulated genes in resistant group of pre-treatment samples. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

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

Hallmark, KEGG and GOBP enrichment results for down-regulated genes in resistant group of pre-treatment samples. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window.Complete files can be downloaded from the download section.)

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

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Mechanism analysis of drug resistance-related DEGs for each cell type in the post-treatment samples

Enrichment results for 5 known drug resistance mechanisms in malignant cells and 1 known mechanism in TME cells.The "Signature" column represents the differentially expressed genes (DEGs) used for enrichment. The "Geneset" column represents the genes included in this mechanism. The "Overlap" column represents the number of genes in the "Geneset" that are enriched in the "Signature". The "Enriched Genes" column represents the genes in the "Geneset" that are enriched in the "Signature". (If the image exists, the user can click on it to enlarge it in a new window.)

Enrichment results for 1 known drug resistance mechanisms in TME cells

Mechnism	Pval	FDR	Signature	Geneset	Overlap	Background	Cell type	Enriched Genes
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	37	186	0	23467	B cells	NA
Regulation by the Disease Microenvironment	6.00e-02	6.00e-02	50	186	2	23467	CD4+ T cells	LDHB,MALAT1
Regulation by the Disease Microenvironment	3.40e-01	3.40e-01	52	186	1	23467	CD8+ T cells	TGFB1
Regulation by the Disease Microenvironment	2.10e-01	2.10e-01	108	186	2	23467	cDCs	HNRNPA2B1,MALAT1
Regulation by the Disease Microenvironment	1.70e-01	1.70e-01	177	186	3	23467	Mono_Macro	ZEB2,HNRNPA2B1,MALAT1
Regulation by the Disease Microenvironment	1.00e-02	1.00e-02	56	186	3	23467	NK cells	TGFB1,HNRNPA2B1,MALAT1
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	19	186	0	23467	pDCs	NA
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	1	186	0	23467	Plasma cells	NA

Hallmark, KEGG and GOBP enrichment results for up-regulated genes in resistant group of post-treatment samples. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

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

Hallmark, KEGG and GOBP enrichment results for down-regulated genes in resistant group of post-treatment samples. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

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

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Mechanism analysis of drug resistance-related DEGs for each cell type in one patient or cell lines

This dataset only has one patient or is a cell line dataset, the resistant sample is the post-treatment sample and the sensitive sample is the pre-treatment sample. Enrichment results for 5 known drug resistance mechanisms in malignant cells and 1 known mechanism in TME cells are shown here.The "Signature" column represents the differentially expressed genes (DEGs) used for enrichment. The "Geneset" column represents the genes included in this mechanism. The "Overlap" column represents the number of genes in the "Geneset" that are enriched in the "Signature". The "Enriched Genes" column represents the genes in the "Geneset" that are enriched in the "Signature". (If the image exists, the user can click on it to enlarge it in a new window.)

Hallmark, KEGG and GOBP enrichment results for up-regulated genes in resistant group. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

Hallmark, KEGG and GOBP enrichment results for down-regulated genes in resistant group. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

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MicroRNAs (miRNAs) regulating drug resistance-related DEGs for malignant cells

In the pre-treatment samples, the miRNAs with a score greater than 80 that regulate the top10 abs(avg_log2FC) drug resistance-related DEGs for malignant cells are shown here. If the gene does not have any miRNAs with a score greater than 80, it will not be shown. Here only the names of miRNAs with a score greater than 90 are shown, but some names will not be shown because of too many overlaps. (Complete files containing all datasets and cell types can be downloaded from the download section.)

Regulating up-regulated DEGs in resistant group	Regulating down-regulated DEGs in resistant group
This dataset does not contain malignant cells, nor does it predict any miRNA that corresponds to the top10 DEGs.	This dataset does not contain malignant cells, nor does it predict any miRNA that corresponds to the top10 DEGs.

In the post-treatment samples, the miRNAs with a score greater than 80 that regulate the top10 abs(avg_log2FC) drug resistance-related DEGs for Malignant cells are shown here. If the gene does not have any miRNAs with a score greater than 80, it will not be shown. Here only the names of miRNAs with a score greater than 90 are shown, but some names will not be shown because of too many overlaps. (Complete files containing all datasets and cell types can be downloaded from the download section.)

Regulating up-regulated DEGs in resistant group	Regulating down-regulated DEGs in resistant group
This dataset does not contain malignant cells, nor does it predict any miRNA that corresponds to the top10 DEGs.	This dataset does not contain malignant cells, nor does it predict any miRNA that corresponds to the top10 DEGs.

This dataset only has one patient or is a cell line dataset, the resistant sample is the post-treatment sample and the sensitive sample is the pre-treatment sample. The miRNAs with a score greater than 80 that regulate the top10 abs(avg_log2FC) drug resistance-related DEGs for Malignant cells are shown here. Here only the names of miRNAs with a score greater than 80 are shown, but some names will not be shown because of too many overlaps. If the gene does not have any miRNAs with a score greater than 90, it will not be shown. (Complete files containing all datasets and cell types can be downloaded from the download section.)

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Motifs and transcription factors (TFs) regulating drug resistance-related DEGs for each cell type

In the pre-treatment samples, the motifs and TFs that regulate drug resistance-related DEGs for each cell type are shown here. (Complete files can be downloaded from the download section.)

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

motif	motif	NES	AUC	TF_highConf	Cell_type
	taipale_tf_pairs__ELK1_FOXI1_RSCGGAANRWMAACAN_CAP_repr	6.31	0.193	ELK1; FOXI1 (directAnnotation).	B cells
	metacluster_48.4	4.91	0.155	GFI1; GFI1; GFI1B; GFI1B; GFI1B (directAnnotation). GFI1; GFI1 (inferredBy_Orthology).	B cells
	transfac_pro__M05507	4.88	0.154	IKZF3 (directAnnotation).	B cells
	transfac_pro__M06423	4.87	0.154	ZNF571 (directAnnotation).	B cells
	transfac_pro__M05522	4.78	0.152	ZNF341 (directAnnotation).	B cells
	metacluster_2.9	4.67	0.149	IRF2; IRF2; IRF2; PRDM1; PRDM1 (directAnnotation). PRDM1 (inferredBy_Orthology).	B cells
	transfac_pro__M05844	4.6	0.147	ZNF628 (inferredBy_Orthology).	B cells
	taipale_tf_pairs__CLOCK_BHLHA15_NCACGTGNNNNNCATATGN_CAP	4.56	0.146	BHLHA15; CLOCK (directAnnotation).	B cells
	metacluster_141.4	4.5	0.144	GLIS2 (directAnnotation).	B cells
	swissregulon__hs__HSF2	4.49	0.144	HSF2 (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__TEAD4_HOXA2_RCATTCNNNNNNCATTA_CAP	17.9	0.713	HOXA2; TEAD4 (directAnnotation).	B cells
	transfac_pro__M06818	12.3	0.492	ZNF592 (inferredBy_Orthology).	B cells
	transfac_pro__M06362	12.2	0.487	ZNF730 (directAnnotation).	B cells
	taipale_tf_pairs__TEAD4_HOXA3_RCATTCNNNNNNCATTA_CAP	11.9	0.475	HOXA3; TEAD4 (directAnnotation).	B cells
	metacluster_80.4	11.8	0.471	ZIC3 (directAnnotation).	B cells
	transfac_pro__M05397	11.6	0.466	ZNF444 (directAnnotation).	B cells
	transfac_pro__M06143	11.6	0.465	ZNF16 (directAnnotation).	B cells
	transfac_pro__M06046	11.1	0.446	ZNF195 (directAnnotation).	B cells
	transfac_pro__M05854	11	0.44	ZNF619 (directAnnotation).	B cells
	transfac_pro__M05864	10.9	0.435	ZNF615 (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_168.17	5.98	0.139	ZNF417; ZNF587 (directAnnotation).	B cells
	transfac_pro__M06904	5.72	0.134	ZNF671 (directAnnotation).	B cells
	transfac_pro__M06702	5.15	0.122	ZNF226 (directAnnotation).	B cells
	metacluster_168.9	5.02	0.119	ZNF354B (directAnnotation).	B cells
	metacluster_162.5	4.58	0.11	NR1D1; NR1D1; RORA; RORA; RORA; RORA; RORA; RORC; RORC (directAnnotation). NR1D1; PPARG; RORA; RORC (inferredBy_Orthology).	B cells
	metacluster_38.3	4.53	0.109	STAT6; STAT6 (directAnnotation). STAT6; STAT6 (inferredBy_Orthology).	B cells
	taipale_tf_pairs__ELK1_FOXI1_RSCGGAANRWMAACAN_CAP_repr	4.39	0.106	ELK1; FOXI1 (directAnnotation).	B cells
	transfac_pro__M05304	4.38	0.106	ZBTB5 (directAnnotation).	B cells
	transfac_pro__M05935	4.32	0.105	ZNF382 (directAnnotation).	B cells
	cisbp__M01725	4.32	0.105	SREBF2 (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_79.1	6.78	0.201	ZNF713; ZNF713; ZNF713 (directAnnotation).	B cells
	transfac_pro__M06362	6.31	0.188	ZNF730 (directAnnotation).	B cells
	taipale_tf_pairs__GCM2_FOXI1_TGTTKATRCGGGN_CAP	6.17	0.184	FOXI1; GCM2 (directAnnotation).	B cells
	dbtfbs__ZNF121_HEK293_ENCSR224QDY_merged_N3	6.11	0.182	ZNF121 (directAnnotation).	B cells
	metacluster_84.7	5.74	0.172	RARA (directAnnotation).	B cells
	taipale_tf_pairs__TEAD4_SPIB_RGAATGCGGAAGTN_CAP_1	5.55	0.166	SPIB; TEAD4 (directAnnotation).	B cells
	transfac_pro__M06733	5.48	0.164	RBAK (directAnnotation).	B cells
	metacluster_196.5	5.43	0.163	RXRG (directAnnotation). HNF4A; HNF4A; HNF4G; HNF4G; NR2C1; NR2C1; NR2C2; NR2C2; NR2F2; NR2F2; NR2F6; NR2F6; RXRA; RXRA; RXRB; RXRB; RXRG; RXRG; RXRG (inferredBy_Orthology).	B cells
	transfac_pro__M01217	5.41	0.163	NR4A1 (directAnnotation).	B cells
	transfac_pro__M06411	5.38	0.162	ZNF662 (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
FOS	metacluster_157.2	up	Mono/Macro	post
JUNB	metacluster_157.2	up	Mono/Macro	post
BACH1	metacluster_157.2	down	Mono/Macro	post
JUNB	tfdimers__MD00141	up	CD8+ T cells	pre
JUNB	tfdimers__MD00475	up	CD8+ T cells	pre
JUNB	metacluster_50.1	up	CD8+ T cells	pre
JUNB	metacluster_137.2	up	CD8+ T cells	pre
JUNB	metacluster_157.2	up	CD8+ T cells	pre
ETS1	tfdimers__MD00299	up	CD8+ T cells	pre
ETV6	swissregulon__hs__ETV6	up	cDCs	pre

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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."