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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
IGLV1-47	ENSG00000211648	0.30666	0.00e+00	0.00e+00	0.295	0.074	B cells	pre
RPL39	ENSG00000198918	0.306489	4.01e-39	8.26e-35	0.99	0.999	B cells	pre
SAMSN1	ENSG00000155307	0.303209	5.89e-17	1.21e-12	0.35	0.221	B cells	pre
IGHG3	ENSG00000282184	0.301258	0.00e+00	0.00e+00	0.295	0.091	B cells	pre
CLIC1	ENSG00000226651	0.298528	1.03e-26	2.11e-22	0.762	0.571	B cells	pre
MARCH1	NA	0.297455	0.00e+00	0.00e+00	0.353	0.139	B cells	pre
RPL4	ENSG00000174444	0.294794	7.43e-27	1.53e-22	0.932	0.817	B cells	pre
S100A11	ENSG00000163191	0.294435	2.94e-26	6.05e-22	0.378	0.202	B cells	pre
HLA-C	ENSG00000206435	0.294392	7.16e-25	1.48e-20	0.988	0.943	B cells	pre
NFKBID	ENSG00000167604	0.293846	2.75e-09	5.68e-05	0.344	0.248	B cells	pre
IGLV3-21	ENSG00000211662	0.292964	0.00e+00	0.00e+00	0.417	0.128	B cells	pre
RPL3	ENSG00000100316	0.290316	1.94e-31	3.99e-27	0.987	0.981	B cells	pre
RPL38	ENSG00000172809	0.288304	1.24e-22	2.56e-18	0.901	0.82	B cells	pre
CD70	ENSG00000125726	0.2805	2.22e-31	4.56e-27	0.269	0.119	B cells	pre
EIF2AK2	ENSG00000055332	0.277938	3.66e-32	7.54e-28	0.375	0.192	B cells	pre
RPL37	ENSG00000145592	0.276042	2.15e-23	4.44e-19	0.99	0.997	B cells	pre
CRIP1	ENSG00000213145	0.275988	5.03e-09	1.04e-04	0.651	0.541	B cells	pre
CAPG	ENSG00000042493	0.275535	8.13e-37	1.67e-32	0.442	0.227	B cells	pre
EIF2S3	ENSG00000130741	0.275298	1.45e-36	2.99e-32	0.529	0.291	B cells	pre
PNISR	ENSG00000132424	0.271666	1.34e-29	2.76e-25	0.488	0.285	B cells	pre
IGLV1-40	ENSG00000274575	0.270921	0.00e+00	0.00e+00	0.407	0.103	B cells	pre
MYL12A	ENSG00000101608	0.266414	7.56e-17	1.56e-12	0.858	0.719	B cells	pre
IGLV4-69	ENSG00000211637	0.262963	0.00e+00	0.00e+00	0.385	0.09	B cells	pre
RPSA	ENSG00000168028	0.261182	1.91e-22	3.94e-18	0.977	0.974	B cells	pre
EIF4B	ENSG00000063046	0.258383	4.69e-32	9.67e-28	0.478	0.267	B cells	pre
TRAF3IP3	ENSG00000009790	0.254116	1.62e-34	3.33e-30	0.299	0.135	B cells	pre
RPL17	ENSG00000265681	0.254023	9.49e-24	1.95e-19	0.981	0.975	B cells	pre
LSP1	ENSG00000288199	0.251128	3.12e-16	6.42e-12	0.693	0.503	B cells	pre
CXCR4	ENSG00000121966	-0.252466	7.10e-12	1.46e-07	0.782	0.855	B cells	pre
IRF1	ENSG00000125347	-0.256281	6.80e-07	1.40e-02	0.35	0.422	B cells	pre
SKIL	ENSG00000136603	-0.259422	2.33e-10	4.81e-06	0.344	0.438	B cells	pre
ANKRD37	ENSG00000186352	-0.264423	3.39e-10	6.99e-06	0.182	0.283	B cells	pre
TCP1	ENSG00000120438	-0.268365	1.26e-15	2.60e-11	0.203	0.339	B cells	pre
TUBB4B	ENSG00000188229	-0.271653	4.45e-10	9.16e-06	0.304	0.4	B cells	pre
MARCKSL1	ENSG00000175130	-0.27495	2.18e-06	4.50e-02	0.314	0.369	B cells	pre
PTGES3	ENSG00000110958	-0.275737	1.85e-10	3.80e-06	0.516	0.572	B cells	pre
PRDX1	ENSG00000117450	-0.279803	1.48e-07	3.06e-03	0.471	0.509	B cells	pre
SMAP2	ENSG00000084070	-0.282313	2.83e-09	5.83e-05	0.459	0.52	B cells	pre
HSPA4	ENSG00000170606	-0.282861	3.59e-17	7.39e-13	0.167	0.307	B cells	pre
FKBP4	ENSG00000004478	-0.285362	4.96e-19	1.02e-14	0.105	0.25	B cells	pre
POMP	ENSG00000132963	-0.28638	4.61e-13	9.49e-09	0.358	0.455	B cells	pre
CREM	ENSG00000095794	-0.287978	4.09e-16	8.42e-12	0.493	0.631	B cells	pre
TAF1D	ENSG00000166012	-0.29135	6.90e-11	1.42e-06	0.375	0.455	B cells	pre
PNRC1	ENSG00000146278	-0.292278	2.72e-12	5.60e-08	0.767	0.768	B cells	pre
SRSF7	ENSG00000115875	-0.294948	1.35e-10	2.78e-06	0.549	0.593	B cells	pre
CKS2	ENSG00000123975	-0.296918	2.75e-09	5.67e-05	0.233	0.324	B cells	pre
ACTB	ENSG00000075624	-0.300301	7.15e-13	1.47e-08	0.997	0.999	B cells	pre
TUBA4A	ENSG00000127824	-0.30375	8.78e-12	1.81e-07	0.307	0.409	B cells	pre
RGS16	ENSG00000143333	-0.305211	2.80e-14	5.78e-10	0.15	0.28	B cells	pre
ATP6V0C	ENSG00000185883	-0.308264	6.69e-11	1.38e-06	0.451	0.517	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
IFI6	ENSG00000126709	1.55119	0.00e+00	0.00e+00	0.717	0.053	Plasma cells	post
IGHG1	ENSG00000277633	1.36472	7.51e-12	1.55e-07	0.824	0.868	Plasma cells	post
HLA-B	ENSG00000206450	1.0908	1.36e-33	2.80e-29	0.945	0.694	Plasma cells	post
IGHGP	ENSG00000282094	1.08391	1.26e-15	2.59e-11	0.394	0.099	Plasma cells	post
IFI27	ENSG00000275214	1.06842	4.36e-25	8.98e-21	0.342	0.02	Plasma cells	post
IGHG4	ENSG00000277016	1.03767	1.11e-15	2.29e-11	0.544	0.22	Plasma cells	post
IFITM1	ENSG00000185885	0.866397	1.03e-28	2.12e-24	0.524	0.102	Plasma cells	post
SQSTM1	ENSG00000284099	0.855623	5.41e-10	1.12e-05	0.638	0.48	Plasma cells	post
NEAT1	ENSG00000245532	0.838952	4.90e-08	1.01e-03	0.651	0.48	Plasma cells	post
MIR155HG	ENSG00000234883	0.772764	3.89e-12	8.02e-08	0.384	0.141	Plasma cells	post
ISG15	ENSG00000187608	0.719153	7.90e-22	1.63e-17	0.332	0.033	Plasma cells	post
JSRP1	ENSG00000167476	0.650994	2.09e-09	4.31e-05	0.541	0.345	Plasma cells	post
PPP1R15A	ENSG00000087074	0.59857	5.80e-10	1.20e-05	0.508	0.289	Plasma cells	post
CDKN1A	ENSG00000124762	0.587697	7.89e-10	1.63e-05	0.42	0.211	Plasma cells	post
SDC1	ENSG00000115884	0.583947	4.99e-22	1.03e-17	0.528	0.171	Plasma cells	post
MT-ND5	ENSG00000198786	0.571419	1.55e-08	3.19e-04	0.795	0.622	Plasma cells	post
CYTOR	ENSG00000222041	0.545642	2.32e-08	4.79e-04	0.564	0.378	Plasma cells	post
TRIB1	ENSG00000173334	0.522659	3.50e-13	7.22e-09	0.469	0.211	Plasma cells	post
PECAM1	ENSG00000261371	0.512269	1.01e-23	2.08e-19	0.42	0.072	Plasma cells	post
ANKRD28	ENSG00000206560	0.494396	2.44e-10	5.03e-06	0.528	0.286	Plasma cells	post
PTP4A3	ENSG00000275575	0.465205	1.07e-18	2.21e-14	0.251	0.01	Plasma cells	post
GAS6	ENSG00000183087	0.451918	3.08e-20	6.34e-16	0.492	0.148	Plasma cells	post
FOSB	ENSG00000125740	0.43585	1.55e-07	3.20e-03	0.541	0.319	Plasma cells	post
MIR4435-2HG	ENSG00000172965	0.422109	4.48e-10	9.23e-06	0.332	0.128	Plasma cells	post
SPAG4	ENSG00000061656	0.380464	2.64e-12	5.44e-08	0.407	0.161	Plasma cells	post
TYMP	ENSG00000025708	0.37021	1.24e-14	2.55e-10	0.29	0.056	Plasma cells	post
CFLAR	ENSG00000003402	0.364042	7.11e-08	1.46e-03	0.371	0.191	Plasma cells	post
HLA-C	ENSG00000206435	0.347528	7.31e-08	1.51e-03	0.964	0.964	Plasma cells	post
LGALS1	ENSG00000100097	0.30613	1.96e-06	4.04e-02	0.264	0.112	Plasma cells	post
IRF7	ENSG00000276561	0.290687	2.87e-08	5.91e-04	0.287	0.112	Plasma cells	post
MANEA	ENSG00000172469	-0.251591	8.93e-09	1.84e-04	0.101	0.283	Plasma cells	post
PTGES3	ENSG00000110958	-0.253238	6.28e-08	1.29e-03	0.104	0.276	Plasma cells	post
CTSS	ENSG00000163131	-0.253838	7.52e-09	1.55e-04	0.081	0.253	Plasma cells	post
RBM3	ENSG00000102317	-0.257513	4.10e-09	8.45e-05	0.075	0.25	Plasma cells	post
NPM1	ENSG00000181163	-0.264767	5.58e-07	1.15e-02	0.134	0.306	Plasma cells	post
JUND	ENSG00000130522	-0.267123	5.24e-07	1.08e-02	0.163	0.342	Plasma cells	post
SEC14L1	ENSG00000129657	-0.269209	5.91e-08	1.22e-03	0.156	0.342	Plasma cells	post
EIF2AK4	ENSG00000128829	-0.271819	2.23e-07	4.59e-03	0.156	0.329	Plasma cells	post
TRMT112	ENSG00000173113	-0.275835	3.20e-10	6.59e-06	0.121	0.336	Plasma cells	post
HINT1	ENSG00000169567	-0.278583	3.54e-08	7.29e-04	0.098	0.273	Plasma cells	post
REEP5	ENSG00000129625	-0.28558	1.81e-07	3.72e-03	0.199	0.382	Plasma cells	post
PNRC1	ENSG00000146278	-0.286898	1.85e-07	3.82e-03	0.091	0.25	Plasma cells	post
RNGTT	ENSG00000111880	-0.289245	2.92e-08	6.02e-04	0.085	0.25	Plasma cells	post
RPN1	ENSG00000163902	-0.291789	5.60e-07	1.15e-02	0.29	0.47	Plasma cells	post
TMED9	ENSG00000184840	-0.292046	2.34e-07	4.83e-03	0.322	0.513	Plasma cells	post
EAF2	ENSG00000145088	-0.29261	5.45e-09	1.12e-04	0.147	0.349	Plasma cells	post
TCEA1	ENSG00000187735	-0.298116	3.67e-10	7.56e-06	0.078	0.266	Plasma cells	post
MZT2B	ENSG00000152082	-0.304844	1.08e-13	2.23e-09	0.062	0.296	Plasma cells	post
NCF1	ENSG00000158517	-0.306695	8.59e-09	1.77e-04	0.107	0.293	Plasma cells	post
LMAN2	ENSG00000169223	-0.307017	2.44e-07	5.02e-03	0.358	0.543	Plasma 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	1.80e-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."