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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 (This dataset does not contain this module)
	Comparison of intra-tumor heterogeneity (ITH) and epithelial-mesenchymal transition (EMT) scores of malignant cells between the resistant and sensitive groups
	Difference of cell-cell interactions between the resistant and sensitive groups (This dataset does not contain this module)
	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 (This dataset does not contain this module)

Dataset: GSE161195

Dataset summary for GSE161195

Datast information	Dataset	GSE161195
	PMID	33619369
	Raw data ID/link	PRJNA675855
	Organism	Homo sapiens
	Source	patients
	Tissue	Bone marrow aspirate
	Cancer type level1	Multiple myeloma
	Cancer type level2	Refractory multiple myeloma (MM)
	Regimen	DARA-KRD (daratumumab + carfilzomib + lenalidomide + dexamethasone)
	Drug type	Targeted therapy
	Sample size	pre (resistant 7, sensitive 21); post (resistant 5, sensitive 15)
	Cell number	36505
	Extract protocol	MARS-seq v2.0
	Data processing	NA
	Public date	Public on Jan 27, 2021
	Description	This dataset has 28 patients, 19 of whom have both pre- and post-treatment samples.

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Drug summary for GSE161195

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"Daratumumab"	DB09331	biotech	CD38	P28907
"Carfilzomib"	DB08889	small molecule	PSMB5; PSMB8; PSMB1; PSMB9; PSMB2; PSMB10	P28074; P28062; P20618; P28065; P49721; P40306
"Lenalidomide"	DB00480	small molecule	CRBN; TNFSF11; CDH5; PTGS2	Q96SW2; O14788; P33151; P35354
"Dexamethasone"	DB01234	small molecule	NR3C1; NR0B1; ANXA1; NOS2; NR1I2	P04150; P51843; P04083; P35228; 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.)

Comparison of ITH scores

Comparison of EMT scores

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Difference of cell-cell interactions between the resistant and sensitive groups

In the pre-treatment samples, the difference in cell-cell interactions between the resistant and sensitive groups was compared. The numbers indicate the count of cell-cell interactions that were either higher or lower in the resistant group compared to the sensitive group. The dot plots of significant ligand-receptor pairs in the resistant group and sensitive group are subsequently displayed. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

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.)

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
ST6GAL1	ENSG00000073849	-0.285404	0.00e+00	0.00e+00	0.108	0.27	Malignant cells	pre
RPS2	ENSG00000140988	-0.286093	4.57e-32	8.44e-28	0.641	0.659	Malignant cells	pre
HDLBP	ENSG00000115677	-0.288657	0.00e+00	0.00e+00	0.231	0.375	Malignant cells	pre
SEL1L	ENSG00000071537	-0.289275	0.00e+00	0.00e+00	0.319	0.443	Malignant cells	pre
PECAM1	ENSG00000261371	-0.295039	0.00e+00	0.00e+00	0.127	0.285	Malignant cells	pre
SNORD35A	ENSG00000200259	-0.299506	0.00e+00	0.00e+00	0.331	0.444	Malignant cells	pre
LINC01781	ENSG00000234184	-0.299714	0.00e+00	0.00e+00	0.099	0.259	Malignant cells	pre
HSPA5	ENSG00000044574	-0.304376	6.96e-24	1.29e-19	0.565	0.619	Malignant cells	pre
ADA2	ENSG00000093072	-0.306925	0.00e+00	0.00e+00	0.078	0.252	Malignant cells	pre
DNAJB9	ENSG00000128590	-0.308889	0.00e+00	0.00e+00	0.189	0.352	Malignant cells	pre
NOP53	ENSG00000105373	-0.311968	0.00e+00	0.00e+00	0.167	0.312	Malignant cells	pre
FRZB	ENSG00000162998	-0.321842	0.00e+00	0.00e+00	0.186	0.312	Malignant cells	pre
FKBP11	ENSG00000134285	-0.324492	0.00e+00	0.00e+00	0.446	0.574	Malignant cells	pre
RPS25	ENSG00000280831	-0.328897	0.00e+00	0.00e+00	0.804	0.853	Malignant cells	pre
HLA-B	ENSG00000206450	-0.335907	0.00e+00	0.00e+00	0.889	0.977	Malignant cells	pre
HSP90B1	ENSG00000166598	-0.342671	4.17e-32	7.71e-28	0.92	0.936	Malignant cells	pre
AC034236.1	NA	-0.351869	0.00e+00	0.00e+00	0.336	0.534	Malignant cells	pre
PSAP	ENSG00000197746	-0.356319	0.00e+00	0.00e+00	0.342	0.529	Malignant cells	pre
HERPUD1	ENSG00000051108	-0.373827	0.00e+00	0.00e+00	0.153	0.336	Malignant cells	pre
RPL3P4	ENSG00000232573	-0.393486	0.00e+00	0.00e+00	0.689	0.777	Malignant cells	pre
RPS14	ENSG00000164587	-0.412548	0.00e+00	0.00e+00	0.922	0.919	Malignant cells	pre
BTG2	ENSG00000159388	-0.413389	0.00e+00	0.00e+00	0.171	0.363	Malignant cells	pre
SLAMF7	ENSG00000026751	-0.429255	0.00e+00	0.00e+00	0.243	0.453	Malignant cells	pre
SEL1L3	ENSG00000091490	-0.436943	0.00e+00	0.00e+00	0.127	0.337	Malignant cells	pre
MTRNR2L1	NA	-0.438808	0.00e+00	0.00e+00	0.122	0.311	Malignant cells	pre
FCRLA	ENSG00000132185	-0.441354	0.00e+00	0.00e+00	0.053	0.254	Malignant cells	pre
CD74	ENSG00000019582	-0.447409	0.00e+00	0.00e+00	0.61	0.752	Malignant cells	pre
TPT1	ENSG00000133112	-0.485539	0.00e+00	0.00e+00	0.792	0.854	Malignant cells	pre
SEC62	ENSG00000008952	-0.506678	0.00e+00	0.00e+00	0.24	0.479	Malignant cells	pre
HLA-E	ENSG00000206493	-0.53186	0.00e+00	0.00e+00	0.337	0.58	Malignant cells	pre
ITM2B	ENSG00000136156	-0.532689	0.00e+00	0.00e+00	0.269	0.48	Malignant cells	pre
SSR4	ENSG00000180879	-0.546311	0.00e+00	0.00e+00	0.883	0.974	Malignant cells	pre
SNORA31	ENSG00000199477	-0.554389	0.00e+00	0.00e+00	0.975	0.97	Malignant cells	pre
IGLC1	ENSG00000211675	-0.605314	0.00e+00	0.00e+00	0.819	0.866	Malignant cells	pre
DERL3	ENSG00000274437	-0.609694	0.00e+00	0.00e+00	0.176	0.461	Malignant cells	pre
XBP1	ENSG00000100219	-0.616537	0.00e+00	0.00e+00	0.605	0.76	Malignant cells	pre
CCND1	ENSG00000110092	-0.678379	0.00e+00	0.00e+00	0.176	0.333	Malignant cells	pre
AC012181.2	NA	-0.734495	0.00e+00	0.00e+00	0.281	0.526	Malignant cells	pre
IGLJ2	ENSG00000211676	-0.94548	0.00e+00	0.00e+00	0.182	0.33	Malignant cells	pre
IGHM	ENSG00000282657	-1.33599	0.00e+00	0.00e+00	0.108	0.32	Malignant cells	pre
IGLC2	ENSG00000211677	-1.347	0.00e+00	0.00e+00	0.628	0.696	Malignant cells	pre
IGHG3	ENSG00000282184	-1.51335	0.00e+00	0.00e+00	0.296	0.662	Malignant cells	pre
IGHG2	ENSG00000274497	-1.56764	0.00e+00	0.00e+00	0.18	0.557	Malignant cells	pre
IGLC3	ENSG00000211679	-1.94839	0.00e+00	0.00e+00	0.485	0.6	Malignant cells	pre
IGHG1	ENSG00000277633	-1.94975	0.00e+00	0.00e+00	0.468	0.72	Malignant cells	pre
IGHGP	ENSG00000282094	-2.11312	0.00e+00	0.00e+00	0.448	0.707	Malignant cells	pre
IGHG4	ENSG00000277016	-2.47255	0.00e+00	0.00e+00	0.168	0.547	Malignant cells	pre

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In the post-treatment samples, the differentially expressed genes (|avg_log2FC|>0.25 & p_val_adj<0.05) between the resistant and sensitive groups for each cell type.

Gene symbol	Gene id	avg_log2FC	p_val	p_val_adj	pct.1	pct.2	Cell type	Timepoint
IGHD	ENSG00000278801	3.88358	0.00e+00	0.00e+00	0.252	0.007	Malignant cells	post
JCHAIN	ENSG00000132465	0.972238	0.00e+00	0.00e+00	0.94	0.64	Malignant cells	post
S100A4	ENSG00000196154	0.849569	0.00e+00	0.00e+00	0.49	0.082	Malignant cells	post
HIST1H4C	NA	0.834114	0.00e+00	0.00e+00	0.414	0.199	Malignant cells	post
COX6C	ENSG00000164919	0.832327	0.00e+00	0.00e+00	0.606	0.288	Malignant cells	post
PABPC1	ENSG00000070756	0.809728	0.00e+00	0.00e+00	0.689	0.561	Malignant cells	post
MIF	ENSG00000276701	0.765432	0.00e+00	0.00e+00	0.691	0.436	Malignant cells	post
RPS24	ENSG00000138326	0.750432	0.00e+00	0.00e+00	0.959	0.908	Malignant cells	post
PTMA	ENSG00000187514	0.738801	0.00e+00	0.00e+00	0.697	0.54	Malignant cells	post
KRTCAP2	ENSG00000163463	0.730036	0.00e+00	0.00e+00	0.69	0.437	Malignant cells	post
TUBA1B	ENSG00000123416	0.717852	0.00e+00	0.00e+00	0.494	0.234	Malignant cells	post
S100A6	ENSG00000197956	0.708801	0.00e+00	0.00e+00	0.498	0.134	Malignant cells	post
SNORD100	ENSG00000221500	0.701846	0.00e+00	0.00e+00	0.932	0.894	Malignant cells	post
RPLP0	ENSG00000089157	0.606175	0.00e+00	0.00e+00	0.943	0.839	Malignant cells	post
MTND1P23	ENSG00000225972	0.602079	0.00e+00	0.00e+00	0.87	0.668	Malignant cells	post
IGHA2	ENSG00000276173	0.580539	0.00e+00	0.00e+00	0.505	0.26	Malignant cells	post
RPL30	ENSG00000156482	0.579217	0.00e+00	0.00e+00	0.907	0.855	Malignant cells	post
HDGF	ENSG00000143321	0.572227	0.00e+00	0.00e+00	0.382	0.122	Malignant cells	post
RPS8	ENSG00000142937	0.569094	0.00e+00	0.00e+00	0.967	0.938	Malignant cells	post
RPL27	ENSG00000131469	0.566037	0.00e+00	0.00e+00	0.916	0.824	Malignant cells	post
YBX1	ENSG00000065978	0.556078	0.00e+00	0.00e+00	0.638	0.392	Malignant cells	post
SEC11C	ENSG00000166562	0.551747	0.00e+00	0.00e+00	0.831	0.657	Malignant cells	post
STMN1	ENSG00000117632	0.543521	0.00e+00	0.00e+00	0.341	0.071	Malignant cells	post
CREG1	ENSG00000143162	0.525654	0.00e+00	0.00e+00	0.365	0.093	Malignant cells	post
RPS21	ENSG00000171858	0.524818	0.00e+00	0.00e+00	0.91	0.861	Malignant cells	post
UQCRH	ENSG00000173660	0.522194	0.00e+00	0.00e+00	0.597	0.342	Malignant cells	post
NME2	ENSG00000243678	0.51354	0.00e+00	0.00e+00	0.595	0.401	Malignant cells	post
RPL37A	ENSG00000197756	0.512026	0.00e+00	0.00e+00	0.972	0.946	Malignant cells	post
LDHA	ENSG00000288299	0.504667	0.00e+00	0.00e+00	0.491	0.241	Malignant cells	post
RPS24P8	ENSG00000224094	0.503826	0.00e+00	0.00e+00	0.551	0.245	Malignant cells	post
HINT1	ENSG00000169567	0.495528	0.00e+00	0.00e+00	0.617	0.391	Malignant cells	post
SSBP1	ENSG00000262771	0.493211	0.00e+00	0.00e+00	0.392	0.147	Malignant cells	post
RPL38	ENSG00000172809	0.489956	0.00e+00	0.00e+00	0.866	0.793	Malignant cells	post
RPL22L1	ENSG00000163584	0.484539	0.00e+00	0.00e+00	0.389	0.192	Malignant cells	post
H2AFZ	NA	0.482649	0.00e+00	0.00e+00	0.45	0.214	Malignant cells	post
PSMB4	ENSG00000159377	0.482118	0.00e+00	0.00e+00	0.502	0.241	Malignant cells	post
RAN	ENSG00000132341	0.467445	0.00e+00	0.00e+00	0.499	0.26	Malignant cells	post
COX7C	ENSG00000127184	0.46576	0.00e+00	0.00e+00	0.675	0.485	Malignant cells	post
MT-ATP8	ENSG00000228253	0.460522	3.05e-30	5.63e-26	0.589	0.528	Malignant cells	post
IGHA1	ENSG00000282633	0.458563	1.84e-33	3.39e-29	0.622	0.622	Malignant cells	post
S100A11	ENSG00000163191	0.458141	0.00e+00	0.00e+00	0.375	0.121	Malignant cells	post
S100A10	ENSG00000197747	0.457811	0.00e+00	0.00e+00	0.362	0.101	Malignant cells	post
HSP90AA1	ENSG00000080824	0.447011	0.00e+00	0.00e+00	0.514	0.312	Malignant cells	post
NPM1	ENSG00000181163	0.444221	0.00e+00	0.00e+00	0.586	0.37	Malignant cells	post
RPL35	ENSG00000136942	0.443619	0.00e+00	0.00e+00	0.879	0.809	Malignant cells	post
ENO1	ENSG00000074800	0.439988	0.00e+00	0.00e+00	0.421	0.19	Malignant cells	post
LDHB	ENSG00000111716	0.437307	0.00e+00	0.00e+00	0.455	0.234	Malignant cells	post
PPIA	ENSG00000196262	0.432421	0.00e+00	0.00e+00	0.585	0.375	Malignant cells	post
HNRNPA2B1	ENSG00000122566	0.426911	0.00e+00	0.00e+00	0.486	0.293	Malignant cells	post
CCT3	ENSG00000163468	0.42062	0.00e+00	0.00e+00	0.322	0.086	Malignant 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 5 known drug-resistant mechanisms in malignant cells

Mechnism	Pval	FDR	Signature	Geneset	Overlap	Background	Cell type	Enriched Genes
Unusual Activation of Pro-survival Pathway	5.00e-03	2.50e-02	97	781	9	23467	Malignant cells	HSPA5,CCND1,HSP90B1,FTL,GAPDH,LDHA,TPT1,YBX1,ENO1
Epigenetic Alteration of DNA, RNA or Protein	5.60e-01	1.00e+00	97	455	2	23467	Malignant cells	GAPDH,MT-CO2
Aberration of the Drug's Therapeutic Target	1.00e+00	1.00e+00	97	90	0	23467	Malignant cells
Drug Inactivation by Structure Modification	1.00e+00	1.00e+00	97	27	0	23467	Malignant cells
Irregularity in Drug Uptake and Drug Efflux	1.00e+00	1.00e+00	97	37	0	23467	Malignant cells

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

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

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

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

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

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

Enrichment results for 5 known drug resistance mechanisms in malignant cells

Mechnism	Pval	FDR	Signature	Geneset	Overlap	Background	Cell type	Enriched Genes
Unusual Activation of Pro-survival Pathway	2.80e-05	1.40e-04	194	781	19	23467	Malignant cells	CFLAR,GSTP1,RPS6,S100A4,STMN1,SLC25A5,HSPD1,GAPDH,HMGB2,HSPB1,LDHA,PABPC1,S100A11,SMC4,TPT1,YBX1,ENO1,GNAS,NPM1
Drug Inactivation by Structure Modification	2.10e-02	5.20e-02	194	27	2	23467	Malignant cells	GSTP1,NME1
Aberration of the Drug's Therapeutic Target	5.30e-01	8.80e-01	194	90	1	23467	Malignant cells	NPM1
Epigenetic Alteration of DNA, RNA or Protein	7.30e-01	9.10e-01	194	455	3	23467	Malignant cells	GAPDH,SMC4,MALAT1
Irregularity in Drug Uptake and Drug Efflux	1.00e+00	1.00e+00	194	37	0	23467	Malignant cells

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.

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

Regulating up-regulated DEGs in resistant group	Regulating down-regulated DEGs in resistant group

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

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

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

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
	swissregulon__hs__ETV6	6.28	0.0851	ETV6 (directAnnotation).	Malignant cells
	taipale_tf_pairs__ELF2_NATGCGGAAGTR_HT	5.73	0.0792	ELF2 (directAnnotation).	Malignant cells
	transfac_pro__M06660	5.32	0.0748	ZNF670 (directAnnotation).	Malignant cells
	hdpi__FLI1	4.62	0.0672	FLI1 (directAnnotation).	Malignant cells
	metacluster_141.4	4.51	0.0661	GLIS2 (directAnnotation).	Malignant cells
	taipale_tf_pairs__ETS2_RCCGGAAGTG_HT	4.36	0.0644	ETS2 (directAnnotation).	Malignant cells
	jaspar__MA1483.2	4.15	0.0623	ELF2 (directAnnotation).	Malignant cells
	taipale_tf_pairs__ETV2_DLX3_RSCGGAANNNNNNNTAATKR_CAP_repr	4.13	0.062	DLX3; ETV2 (directAnnotation).	Malignant cells
	metacluster_166.4	4.13	0.062	BCLAF1; EHF; ELF1; ELF1; ELF1; ELF1; ELF1; ELF1; ELF2; ELF2; ELF4; ELK1; ELK1; ELK1; ELK1; ELK1; ELK1; ELK1; ELK1; ELK1; ELK3; ELK3; ELK3; ELK3; ELK4; ERG; ERG; ERG; ERG; ETS1; ETS1; ETS1; ETS1; ETS1; ETV1; ETV1; ETV1; ETV1; ETV2; ETV3; ETV4; ETV4; ETV4; ETV4; ETV4; ETV5; ETV7; FEV; FEV; FLI1; FLI1; FLI1; FLI1; GABPA; GABPA; GABPA; GABPA; GABPA; GABPA; GABPB1; GATAD1; PHF20; ZBTB25; ZBTB40 (directAnnotation). EHF; ELF1; ELF1; ELF3; ELF5; ELK3; ELK4; ERG; ETS1; ETV1; ETV2; ETV4; FLI1; GABPA; GABPA (inferredBy_Orthology).	Malignant cells
	taipale_tf_pairs__ETV5_FOXI1_RSCGGATGTTGN_CAP	3.97	0.0604	ETV5; FOXI1 (directAnnotation).	Malignant 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.)

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."