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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_PacAteTissue

Dataset summary for GSE169246_PacAteTissue

Datast information	Dataset	GSE169246_PacAteTissue
	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	atezolizumab + paclitaxel
	Drug type	Immunotherapy
	Sample size	pre (resistant 5, sensitive 4); post (resistant 4, sensitive 2)
	Cell number	87713
	Extract protocol	10x genomics
	Data processing	CellRanger 3.0.0
	Public date	Public on Sep 15, 2021
	Description	This dataset has 9 patients, 6 of whom have both pre -and post-treatment samples.

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Drug summary for GSE169246_PacAteTissue

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.)

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
IGKV1D-13	ENSG00000276566	3.91167	0.00e+00	0.00e+00	0.329	0.059	Plasma cells	pre
IGHV1-46	ENSG00000282131	3.59974	0.00e+00	0.00e+00	0.273	0.022	Plasma cells	pre
IGHA1	ENSG00000282633	2.23262	0.00e+00	0.00e+00	0.375	0.129	Plasma cells	pre
IGLV1-44	ENSG00000274854	2.09012	0.00e+00	0.00e+00	0.261	0.045	Plasma cells	pre
IGLV3-1	ENSG00000211673	1.81246	0.00e+00	0.00e+00	0.629	0.307	Plasma cells	pre
IGHG2	ENSG00000274497	1.71756	0.00e+00	0.00e+00	0.406	0.116	Plasma cells	pre
MT1X	ENSG00000187193	1.57974	0.00e+00	0.00e+00	0.406	0.141	Plasma cells	pre
IGHG4	ENSG00000277016	1.38447	0.00e+00	0.00e+00	0.504	0.169	Plasma cells	pre
IGLC2	ENSG00000211677	1.36757	8.56e-38	1.76e-33	0.506	0.254	Plasma cells	pre
MT2A	ENSG00000125148	1.28608	8.12e-29	1.67e-24	0.317	0.152	Plasma cells	pre
HLA-B	ENSG00000206450	1.24184	0.00e+00	0.00e+00	0.912	0.673	Plasma cells	pre
NEAT1	ENSG00000245532	1.23377	0.00e+00	0.00e+00	0.658	0.324	Plasma cells	pre
DNAAF1	ENSG00000154099	1.20228	0.00e+00	0.00e+00	0.384	0.085	Plasma cells	pre
IGKV1-9	ENSG00000282758	1.13929	1.36e-39	2.79e-35	0.285	0.095	Plasma cells	pre
IFI6	ENSG00000126709	1.03185	0.00e+00	0.00e+00	0.686	0.339	Plasma cells	pre
GADD45A	ENSG00000116717	0.949821	0.00e+00	0.00e+00	0.451	0.107	Plasma cells	pre
ISG15	ENSG00000187608	0.915304	6.35e-39	1.31e-34	0.376	0.171	Plasma cells	pre
MT-ATP8	ENSG00000228253	0.914344	6.05e-38	1.25e-33	0.824	0.649	Plasma cells	pre
IGLV6-57	ENSG00000211640	0.902826	3.79e-26	7.82e-22	0.258	0.107	Plasma cells	pre
SQSTM1	ENSG00000284099	0.825485	0.00e+00	6.08e-42	0.686	0.441	Plasma cells	pre
MT-ND5	ENSG00000198786	0.805043	0.00e+00	0.00e+00	0.848	0.598	Plasma cells	pre
MIR155HG	ENSG00000234883	0.785093	3.65e-31	7.52e-27	0.472	0.276	Plasma cells	pre
MALAT1	ENSG00000251562	0.770867	5.60e-07	1.15e-02	0.963	0.915	Plasma cells	pre
BTG2	ENSG00000159388	0.754115	5.18e-44	1.07e-39	0.689	0.476	Plasma cells	pre
IGKV3-20	ENSG00000282402	0.741922	0.00e+00	0.00e+00	0.538	0.254	Plasma cells	pre
HIST2H2AA4	NA	0.738999	0.00e+00	0.00e+00	0.381	0.1	Plasma cells	pre
MT-ND6	ENSG00000198695	0.733702	0.00e+00	0.00e+00	0.573	0.229	Plasma cells	pre
IGHGP	ENSG00000282094	0.730723	0.00e+00	0.00e+00	0.365	0.077	Plasma cells	pre
IFI27	ENSG00000275214	0.650647	4.83e-23	9.94e-19	0.373	0.212	Plasma cells	pre
JCHAIN	ENSG00000132465	0.61744	3.58e-36	7.37e-32	0.837	0.542	Plasma cells	pre
JSRP1	ENSG00000167476	0.602757	6.73e-44	1.37e-39	0.478	0.249	Plasma cells	pre
ZFP36	ENSG00000128016	0.577475	1.53e-21	3.15e-17	0.492	0.321	Plasma cells	pre
RGS1	ENSG00000090104	0.566839	8.36e-28	1.72e-23	0.594	0.402	Plasma cells	pre
RHOB	ENSG00000143878	0.562328	3.26e-30	6.73e-26	0.422	0.234	Plasma cells	pre
CYTOR	ENSG00000222041	0.521793	1.32e-23	2.72e-19	0.53	0.35	Plasma cells	pre
PDE4B	ENSG00000184588	0.50108	1.69e-16	3.47e-12	0.412	0.278	Plasma cells	pre
NFKBIA	ENSG00000100906	0.477559	1.87e-22	3.85e-18	0.48	0.308	Plasma cells	pre
PIM2	ENSG00000102096	0.472434	2.24e-34	4.62e-30	0.616	0.395	Plasma cells	pre
CCND2	ENSG00000118971	0.467465	0.00e+00	2.10e-44	0.263	0.069	Plasma cells	pre
ANKRD28	ENSG00000206560	0.465094	0.00e+00	5.38e-43	0.405	0.167	Plasma cells	pre
HSP90B1	ENSG00000166598	0.439049	6.48e-22	1.34e-17	0.906	0.801	Plasma cells	pre
RBM33	ENSG00000184863	0.432925	0.00e+00	1.46e-42	0.26	0.071	Plasma cells	pre
PRDM1	ENSG00000057657	0.43191	1.28e-27	2.65e-23	0.463	0.266	Plasma cells	pre
DERL3	ENSG00000274437	0.426657	9.86e-22	2.03e-17	0.837	0.729	Plasma cells	pre
KLF6	ENSG00000067082	0.418952	1.44e-22	2.96e-18	0.615	0.417	Plasma cells	pre
SDC1	ENSG00000115884	0.413276	0.00e+00	0.00e+00	0.451	0.174	Plasma cells	pre
IGKV1-39	ENSG00000282120	0.409655	4.67e-24	9.62e-20	0.427	0.205	Plasma cells	pre
TPM4	ENSG00000167460	0.409613	8.81e-21	1.81e-16	0.54	0.373	Plasma cells	pre
IGHG1	ENSG00000277633	0.406504	2.83e-13	5.82e-09	0.896	0.898	Plasma cells	pre
FNDC3B	ENSG00000075420	0.406405	8.16e-31	1.68e-26	0.393	0.199	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
LY6E	ENSG00000278032	0.688334	4.40e-11	9.07e-07	0.473	0.206	Mono/Macro	post
C3	ENSG00000125730	0.684398	1.98e-20	4.08e-16	0.39	0.006	Mono/Macro	post
CXCL8	ENSG00000169429	0.670477	2.12e-10	4.37e-06	0.522	0.226	Mono/Macro	post
CTSZ	ENSG00000101160	0.664431	5.62e-09	1.16e-04	0.894	0.781	Mono/Macro	post
EGR1	ENSG00000120738	0.648867	1.96e-10	4.04e-06	0.451	0.168	Mono/Macro	post
S100A6	ENSG00000197956	0.641015	2.03e-15	4.18e-11	0.883	0.568	Mono/Macro	post
HLA-B	ENSG00000206450	0.623738	1.05e-21	2.15e-17	0.999	0.974	Mono/Macro	post
YWHAH	ENSG00000128245	0.621396	3.71e-13	7.65e-09	0.59	0.29	Mono/Macro	post
FCER1G	ENSG00000158869	0.617749	1.66e-14	3.42e-10	0.905	0.735	Mono/Macro	post
SERF2	ENSG00000140264	0.609788	2.53e-24	5.22e-20	0.993	0.987	Mono/Macro	post
TSPO	ENSG00000100300	0.5854	1.26e-15	2.60e-11	0.726	0.413	Mono/Macro	post
FOSB	ENSG00000125740	0.568964	1.72e-09	3.54e-05	0.757	0.503	Mono/Macro	post
FABP5	ENSG00000164687	0.562172	3.88e-10	8.00e-06	0.529	0.258	Mono/Macro	post
RPL41	ENSG00000229117	0.545416	4.51e-11	9.29e-07	0.992	0.968	Mono/Macro	post
SDS	ENSG00000135094	0.54308	1.45e-10	2.98e-06	0.397	0.135	Mono/Macro	post
ATF3	ENSG00000162772	0.53241	1.49e-10	3.07e-06	0.628	0.335	Mono/Macro	post
S100A10	ENSG00000197747	0.521822	2.23e-13	4.59e-09	0.836	0.529	Mono/Macro	post
PSAP	ENSG00000197746	0.520033	1.43e-07	2.95e-03	0.952	0.852	Mono/Macro	post
PLAUR	ENSG00000011422	0.519563	2.19e-10	4.51e-06	0.702	0.406	Mono/Macro	post
S100A4	ENSG00000196154	0.500055	1.53e-11	3.14e-07	0.775	0.465	Mono/Macro	post
UQCR11	ENSG00000127540	0.492062	1.31e-14	2.70e-10	0.76	0.497	Mono/Macro	post
PLXDC2	ENSG00000120594	0.487821	2.18e-14	4.49e-10	0.494	0.174	Mono/Macro	post
ATP6V1F	ENSG00000128524	0.487352	1.06e-09	2.19e-05	0.736	0.555	Mono/Macro	post
DBI	ENSG00000155368	0.48511	3.63e-10	7.48e-06	0.77	0.561	Mono/Macro	post
BRI3	ENSG00000164713	0.474509	3.16e-08	6.51e-04	0.755	0.626	Mono/Macro	post
CKLF	ENSG00000217555	0.467953	7.28e-13	1.50e-08	0.459	0.148	Mono/Macro	post
MIF	ENSG00000276701	0.457931	7.70e-09	1.59e-04	0.664	0.439	Mono/Macro	post
FCGR2B	ENSG00000072694	0.451595	1.06e-10	2.19e-06	0.367	0.103	Mono/Macro	post
TIMP2	ENSG00000035862	0.437957	1.64e-09	3.39e-05	0.506	0.258	Mono/Macro	post
NDUFB2	ENSG00000090266	0.436847	9.90e-12	2.04e-07	0.683	0.413	Mono/Macro	post
GPNMB	ENSG00000136235	0.435405	6.20e-08	1.28e-03	0.592	0.329	Mono/Macro	post
NOP10	ENSG00000182117	0.430127	1.29e-08	2.66e-04	0.554	0.316	Mono/Macro	post
RGS1	ENSG00000090104	0.428034	1.15e-07	2.37e-03	0.437	0.2	Mono/Macro	post
SNX10	ENSG00000086300	0.423033	2.28e-08	4.69e-04	0.502	0.284	Mono/Macro	post
ID2	ENSG00000115738	0.421562	1.54e-08	3.18e-04	0.479	0.239	Mono/Macro	post
SLC16A3	ENSG00000141526	0.420214	3.80e-12	7.83e-08	0.346	0.071	Mono/Macro	post
NEAT1	ENSG00000245532	0.413667	2.56e-10	5.27e-06	0.855	0.574	Mono/Macro	post
SELENOW	ENSG00000178980	0.413474	1.14e-10	2.34e-06	0.424	0.155	Mono/Macro	post
MS4A7	ENSG00000166927	0.412605	5.04e-09	1.04e-04	0.657	0.387	Mono/Macro	post
TYMP	ENSG00000025708	0.405923	2.84e-08	5.86e-04	0.715	0.51	Mono/Macro	post
MSR1	ENSG00000038945	0.398867	5.17e-10	1.06e-05	0.429	0.155	Mono/Macro	post
CCL3	ENSG00000278567	0.398336	2.28e-08	4.70e-04	0.628	0.342	Mono/Macro	post
CYBA	ENSG00000051523	0.39384	3.96e-10	8.17e-06	0.979	0.871	Mono/Macro	post
ATP6V0B	ENSG00000117410	0.3833	7.20e-09	1.48e-04	0.761	0.568	Mono/Macro	post
NDUFS5	ENSG00000168653	0.381785	3.92e-12	8.07e-08	0.45	0.142	Mono/Macro	post
CFD	ENSG00000274619	0.379622	9.54e-09	1.97e-04	0.579	0.31	Mono/Macro	post
FPR3	ENSG00000187474	0.376067	3.15e-08	6.48e-04	0.391	0.168	Mono/Macro	post
CD99	ENSG00000002586	0.374727	4.57e-09	9.42e-05	0.478	0.232	Mono/Macro	post
PPT1	ENSG00000131238	0.368101	3.70e-09	7.63e-05	0.627	0.387	Mono/Macro	post
GRN	ENSG00000030582	0.367724	4.11e-07	8.46e-03	0.862	0.729	Mono/Macro	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	1.80e-01	1.80e-01	182	186	3	23467	B cells	TGFB1,CXCR4,VIM
Regulation by the Disease Microenvironment	8.00e-02	8.00e-02	288	186	5	23467	CD4+ T cells	FYN,GATA3,STAT3,VIM,MALAT1
Regulation by the Disease Microenvironment	2.00e-01	2.00e-01	195	186	3	23467	CD8+ T cells	NFKB1,FYN,VIM
Regulation by the Disease Microenvironment	2.10e-01	2.10e-01	29	186	1	23467	Mast cells	MALAT1
Regulation by the Disease Microenvironment	6.00e-02	6.00e-02	264	186	5	23467	Mono_Macro	MMP9,IL1B,TGFBR1,VIM,TIMP2
Regulation by the Disease Microenvironment	5.60e-02	5.60e-02	181	186	4	23467	NK cells	NFKB1,TGFB1,FYN,MALAT1
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	59	186	0	23467	pDCs	NA
Regulation by the Disease Microenvironment	8.60e-02	8.60e-02	210	186	4	23467	Plasma cells	TP53INP1,CXCR4,RHOB,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
There is no signaficant down-regulated pathways in resistant group

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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	2.10e-02	2.10e-02	347	186	7	23467	B cells	NFKB1,PARP1,PTEN,CCNG2,HNRNPA2B1,SOCS3,LDHB
Regulation by the Disease Microenvironment	1.50e-01	1.50e-01	171	186	3	23467	CD4+ T cells	VIM,LDHB,MALAT1
Regulation by the Disease Microenvironment	1.90e-01	1.90e-01	190	186	3	23467	CD8+ T cells	CXCR4,VIM,MALAT1
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	29	186	0	23467	Mast cells	NA
Regulation by the Disease Microenvironment	9.20e-02	9.20e-02	215	186	4	23467	Mono_Macro	MMP9,HNRNPA2B1,VIM,TIMP2
Regulation by the Disease Microenvironment	6.60e-02	6.60e-02	117	186	3	23467	NK cells	NFKB1,CXCR4,MALAT1
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	15	186	0	23467	pDCs	NA
Regulation by the Disease Microenvironment	6.70e-01	6.70e-01	139	186	1	23467	Plasma cells	MTDH

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__M05513	4.06	0.0867	ZNF641 (inferredBy_Orthology).	B cells
	transfac_pro__M05352	4.04	0.0865	ZNF692 (inferredBy_Orthology).	B cells
	transfac_pro__M06257	4	0.0858	ZNF616 (directAnnotation).	B cells
	kznf__ZNF184_Schmitges2016_RCADE	3.99	0.0857	ZNF184 (directAnnotation).	B cells
	metacluster_103.2	3.96	0.0852	ZNF136; ZNF680 (directAnnotation).	B cells
	transfac_pro__M06952	3.94	0.0849	BATF (directAnnotation).	B cells
	transfac_pro__M06360	3.73	0.0818	ZNF626 (directAnnotation).	B cells
	transfac_pro__M01721	3.69	0.0812	PURA (directAnnotation).	B cells
	cisbp__M01738	3.68	0.081	BHLHE40 (inferredBy_Orthology).	B cells
	hocomoco__SMAD3_HUMAN.H11MO.0.B	3.68	0.081	SMAD3 (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
	transfac_pro__M05550	6.29	0.128	SNAPC4 (inferredBy_Orthology).	B cells
	jaspar__MA0604.1	5.39	0.113	ATF1 (inferredBy_Orthology).	B cells
	metacluster_21.5	5.11	0.109	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	5.07	0.108	HSF1; HSF1; HSF2 (directAnnotation). HSF1; HSF2; HSF4; HSF5; HSFX1; HSFX2; HSFX3; HSFX4; HSFY1; HSFY2 (inferredBy_Orthology).	B cells
	metacluster_21.4	4.87	0.105	HSF1; HSF1; HSF2 (directAnnotation). HSF1; HSF2; HSF4; HSF5; HSFX1; HSFX2; HSFX3; HSFX4; HSFY1; HSFY2 (inferredBy_Orthology).	B cells
	transfac_public__M00039	4.86	0.105	CREB1 (directAnnotation).	B cells
	dbtfbs__GMEB1_K562_ENCSR928KOR_merged_N1	4.69	0.102	GMEB1 (directAnnotation).	B cells
	transfac_pro__M04826	4.64	0.101	EP300 (directAnnotation).	B cells
	transfac_pro__M05976	4.62	0.101	ZNF223 (directAnnotation).	B cells
	transfac_pro__M01861	4.49	0.0987	ATF1 (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_2.8	6.15	0.0952	IRF4; IRF5; IRF6; IRF9 (directAnnotation). IRF3; IRF5; IRF5; IRF6 (inferredBy_Orthology).	B cells
	dbtfbs__GMEB1_K562_ENCSR928KOR_merged_N1	5.78	0.0911	GMEB1 (directAnnotation).	B cells
	jaspar__MA0604.1	5.65	0.0897	ATF1 (inferredBy_Orthology).	B cells
	taipale_cyt_meth__CREB1_NRTGACGTN_eDBD_repr	5.35	0.0865	CREB1 (directAnnotation).	B cells
	metacluster_2.9	5.11	0.0837	IRF2; IRF2; IRF2; PRDM1; PRDM1 (directAnnotation). PRDM1 (inferredBy_Orthology).	B cells
	metacluster_22.25	4.98	0.0824	NFE2L2 (directAnnotation).	B cells
	metacluster_22.18	4.77	0.0801	BACH2 (inferredBy_Orthology).	B cells
	transfac_pro__M08803	4.73	0.0796	CREM (directAnnotation).	B cells
	kznf__ZNF613_Imbeault2017_RP_RCADE	4.61	0.0783	ZNF613 (directAnnotation).	B cells
	metacluster_22.29	4.58	0.078	NFE2 (directAnnotation).	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
	dbtfbs__ZNF407_representative_N1	4.03	0.1	ZNF407 (directAnnotation).	B cells
	metacluster_144.3	4.01	0.0997	ZNF704; ZNF704 (directAnnotation).	B cells
	transfac_pro__M12697	3.98	0.0993	ZNF142 (directAnnotation).	B cells
	metacluster_151.2	3.95	0.0987	ZNF23 (directAnnotation).	B cells
	cisbp__M00341	3.87	0.0974	PAX6 (directAnnotation).	B cells
	kznf__ZNF383_Imbeault2017_OM_RCADE	3.76	0.0956	ZNF383 (directAnnotation).	B cells
	kznf__ZNF730_Imbeault2017_RP_RCADE	3.75	0.0953	ZNF730 (directAnnotation).	B cells
	transfac_pro__M06035	3.73	0.095	ZNF749 (directAnnotation).	B cells
	metacluster_141.5	3.69	0.0944	NR3C1; THAP1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY2; YY2; ZNF597 (directAnnotation). YY1; YY1; YY1; YY2; ZFP42 (inferredBy_Orthology).	B cells
	cisbp__M07938	3.68	0.0942	E2F1 (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
STAT1	metacluster_2.6	up	B cells	post
CREM	transfac_pro__M00801	up	B cells	post
IRF1	tfdimers__MD00026	up	B cells	post
IRF1	metacluster_2.7	up	B cells	post
IRF7	metacluster_2.7	up	B cells	post
STAT1	metacluster_2.7	up	B cells	post
STAT1	metacluster_38.1	up	B cells	post
KLF10	metacluster_170.2	up	B cells	post
KLF10	metacluster_163.1	up	B cells	post
EGR1	metacluster_55.3	up	B 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."