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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
	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 (This dataset does not contain this module)
	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: GSE207422_Tor

Dataset summary for GSE207422_Tor

Datast information	Dataset	GSE207422_Tor
	PMID	36869384
	Raw data ID/link	https://ngdc.cncb.ac.cn/gsa-human/browse/HRA001033
	Organism	Homo sapiens
	Source	patients
	Tissue	Tumor tissue
	Cancer type level1	Lung cancer
	Cancer type level2	EGFR/ALK mutation negative non-small cell lung cancer (NSCLC)
	Regimen	toripalimab + carboplatin + (docetaxel or pemetrexed or emcitabine)
	Drug type	Immunotherapy
	Sample size	post (resistant 3, sensitive 2)
	Cell number	8690
	Extract protocol	BD Rhapsody system
	Data processing	BD Rhapsody Whole Transcriptome Analysis (WTA) Pipeline
	Public date	Public on Mar 21, 2023
	Description	This dataset has 5 patients with post-treatment samples.

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Drug summary for GSE207422_Tor

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"Toripalimab"	DB15043	biotech	PDCD1	Q15116
"carboplatin" is not included in the drug list.
"Docetaxel"	DB01248	small molecule	TUBB1; MAP2; MAP4; MAPT; BCL2; NR1I2	Q9H4B7; P11137; P27816; P10636; P10415; O75469
"Pemetrexed"	DB00642	small molecule	TYMS; ATIC; DHFR; GART	P04818; P31939; P00374; P22102
"emcitabine" is not included in the drug list.

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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.)

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.

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
SNRPD1	ENSG00000167088	0.335167	1.16e-07	2.62e-03	0.445	0.319	Malignant cells	post
RTN3	ENSG00000133318	0.334251	1.52e-16	3.41e-12	0.482	0.237	Malignant cells	post
PSMB2	ENSG00000126067	0.334197	5.24e-17	1.18e-12	0.556	0.301	Malignant cells	post
QSOX1	ENSG00000116260	0.334151	2.09e-18	4.69e-14	0.291	0.077	Malignant cells	post
NDUFB2	ENSG00000090266	0.333206	1.05e-17	2.36e-13	0.582	0.325	Malignant cells	post
ZFAND5	ENSG00000107372	0.332659	1.75e-17	3.94e-13	0.541	0.281	Malignant cells	post
HEBP2	ENSG00000051620	0.329892	2.60e-10	5.84e-06	0.344	0.18	Malignant cells	post
EFHD2	ENSG00000142634	0.329485	3.66e-21	8.23e-17	0.25	0.037	Malignant cells	post
P4HB	ENSG00000185624	0.329129	5.31e-14	1.19e-09	0.745	0.567	Malignant cells	post
RAB7A	ENSG00000075785	0.328804	8.92e-12	2.00e-07	0.691	0.567	Malignant cells	post
BCL9L	ENSG00000186174	0.328553	5.90e-19	1.32e-14	0.256	0.053	Malignant cells	post
RPL24	ENSG00000114391	0.328302	5.83e-16	1.31e-11	0.908	0.833	Malignant cells	post
ITGA6	ENSG00000091409	0.327323	2.26e-10	5.08e-06	0.275	0.123	Malignant cells	post
RSRC1	ENSG00000174891	0.327082	2.35e-15	5.29e-11	0.298	0.103	Malignant cells	post
RBMS1	ENSG00000153250	0.326012	4.90e-20	1.10e-15	0.297	0.07	Malignant cells	post
NCOR2	ENSG00000196498	0.325386	2.62e-18	5.88e-14	0.253	0.055	Malignant cells	post
MLPH	ENSG00000115648	0.325006	2.94e-20	6.61e-16	0.268	0.051	Malignant cells	post
SLC39A7	ENSG00000229802	0.324075	1.01e-18	2.27e-14	0.355	0.121	Malignant cells	post
CHP1	ENSG00000187446	0.323625	1.21e-20	2.73e-16	0.272	0.055	Malignant cells	post
COMMD6	ENSG00000188243	0.322934	6.57e-22	1.48e-17	0.396	0.123	Malignant cells	post
RDX	ENSG00000137710	0.322439	9.83e-20	2.21e-15	0.357	0.112	Malignant cells	post
PDIA4	ENSG00000155660	0.320398	1.41e-11	3.18e-07	0.397	0.213	Malignant cells	post
RAB27A	ENSG00000069974	0.32036	1.17e-20	2.64e-16	0.3	0.068	Malignant cells	post
TERF2IP	ENSG00000166848	0.318999	6.79e-20	1.53e-15	0.323	0.092	Malignant cells	post
TUBA4A	ENSG00000127824	0.318819	6.45e-17	1.45e-12	0.278	0.077	Malignant cells	post
STX12	ENSG00000117758	0.317713	1.37e-22	3.07e-18	0.258	0.035	Malignant cells	post
SAMD4B	ENSG00000179134	0.31756	4.17e-17	9.37e-13	0.314	0.101	Malignant cells	post
CALM2	ENSG00000143933	0.317431	7.66e-13	1.72e-08	0.799	0.615	Malignant cells	post
HSDL2	ENSG00000119471	0.317169	9.24e-24	2.08e-19	0.306	0.057	Malignant cells	post
TMED3	ENSG00000166557	0.316747	3.62e-18	8.14e-14	0.396	0.156	Malignant cells	post
HSPA8	ENSG00000109971	0.316289	1.81e-09	4.06e-05	0.771	0.642	Malignant cells	post
NECTIN2	ENSG00000130202	0.315842	1.76e-20	3.97e-16	0.263	0.048	Malignant cells	post
RBM17	ENSG00000134453	0.315315	2.81e-13	6.32e-09	0.335	0.145	Malignant cells	post
EEF1D	ENSG00000273594	0.314546	4.71e-15	1.06e-10	0.611	0.374	Malignant cells	post
ARPC3	ENSG00000111229	0.314234	1.61e-18	3.61e-14	0.394	0.145	Malignant cells	post
ZNF706	ENSG00000120963	0.313438	2.82e-08	6.34e-04	0.371	0.24	Malignant cells	post
MLEC	ENSG00000110917	0.312256	1.39e-15	3.13e-11	0.287	0.092	Malignant cells	post
DAZAP2	ENSG00000183283	0.310428	2.23e-21	5.02e-17	0.464	0.174	Malignant cells	post
DUOXA1	ENSG00000140254	0.309856	1.73e-21	3.90e-17	0.278	0.053	Malignant cells	post
SEC61B	ENSG00000106803	0.309696	6.28e-21	1.41e-16	0.443	0.165	Malignant cells	post
WNK1	ENSG00000060237	0.309632	2.06e-18	4.63e-14	0.335	0.105	Malignant cells	post
YME1L1	ENSG00000136758	0.30953	1.08e-15	2.42e-11	0.352	0.141	Malignant cells	post
OAZ1	ENSG00000104904	0.308852	3.00e-19	6.74e-15	0.868	0.705	Malignant cells	post
CLIC1	ENSG00000226651	0.308198	2.54e-16	5.70e-12	0.386	0.158	Malignant cells	post
BRD2	ENSG00000234704	0.307055	1.30e-11	2.92e-07	0.588	0.409	Malignant cells	post
SRPRA	ENSG00000182934	0.306327	5.51e-21	1.24e-16	0.314	0.075	Malignant cells	post
ITPKC	ENSG00000086544	0.305298	1.14e-16	2.57e-12	0.285	0.084	Malignant cells	post
PDIA3	ENSG00000167004	0.305163	2.79e-12	6.27e-08	0.703	0.541	Malignant cells	post
RAB11B	ENSG00000185236	0.305079	5.22e-16	1.17e-11	0.504	0.262	Malignant cells	post
YAP1	ENSG00000137693	0.303744	1.99e-16	4.47e-12	0.355	0.138	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.)

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.)

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.)

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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	1.00e-22	5.10e-22	945	781	96	23467	Malignant cells	PPP2R5A,ANXA2,AREG,BCL11A,CDKN1A,CERS2,DUSP6,EGFR,GSTP1,SLC2A1,HEY1,HSPA1A,IFI27,ISG15,JUN,PKM,MUC1,MYC,NFE2L2,RAB12,RHOA,RPS6,SOX2,TRIM16,YAP1,SLC25A5,AGR2,ANXA1,NET1,BAG3,HSPA5,ALCAM,CD44,CDKN2A,HSPD1,CLTC,CLU,CAPNS1,CTNND1,DDR1,DUSP1,EGR1,ERRFI1,EZR,FTL,GAPDH,GCLM,GCLC,GSR,HAX1,HBEGF,HSPA8,HK1,NFKBIA,ITGB1,ITGB8,TCF4,AK4,KLF4,LAMP2,LAMP3,LDHA,LRRFIP1,MTDH,NOTCH3,NQO1,NTRK2,TP63,PABPC1,PDCD10,PGK1,POMP,RAB27A,ERBB3,RND3,HNRNPA1,S100A11,TMED3,TMEM54,TNFSF10,TOP1,TUSC3,USP14,WNT5A,ENO1,SLC16A1,CALR,NPM1,CEBPD,DHCR24,GFPT1,INSIG1,BRD2,NKX2-1,FZD7,ALDH1A1
Irregularity in Drug Uptake and Drug Efflux	3.30e-03	8.40e-03	945	37	6	23467	Malignant cells	SLC2A1,ABCC1,ABCE1,ABCG1,ABCC5,SLC34A2
Drug Inactivation by Structure Modification	9.30e-02	1.60e-01	945	27	3	23467	Malignant cells	GSTP1,CES1,CMPK1
Aberration of the Drug's Therapeutic Target	3.00e-01	3.70e-01	945	90	5	23467	Malignant cells	EGFR,CDKN2A,NPM1,NECTIN4,LRRK2
Epigenetic Alteration of DNA, RNA or Protein	9.80e-01	9.80e-01	945	455	11	23467	Malignant cells	EGFR,H2AFY,LMNA,PMAIP1,CDKN2A,GAPDH,MALAT1,GDI2,PPP1R15A,MT-CO2,MX1

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	2.90e-01	2.90e-01	239	186	3	23467	B cells	PAK1,CXCR4,MALAT1
Regulation by the Disease Microenvironment	1.80e-02	1.80e-02	126	186	4	23467	CD4+ T cells	CXCR4,JAK3,RHOB,VIM
Regulation by the Disease Microenvironment	6.20e-02	6.20e-02	114	186	3	23467	CD8+ T cells	CXCR4,RHOB,VIM
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	8	186	0	23467	Endothelial cells	NA
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	9	186	0	23467	Fibroblasts	NA
Regulation by the Disease Microenvironment	4.10e-02	4.10e-02	238	186	5	23467	Mono_Macro	VEGFA,CXCR4,IL1B,SOCS3,MALAT1
Regulation by the Disease Microenvironment	1.90e-02	1.90e-02	193	186	5	23467	Neutrophils	PTEN,IL1B,SOCS3,VIM,TIMP2
Regulation by the Disease Microenvironment	3.00e-01	3.00e-01	44	186	1	23467	pDCs	CXCR4
Regulation by the Disease Microenvironment	2.30e-02	2.30e-02	76	186	3	23467	Plasma cells	TP53INP1,CXCR4,VIM

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

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

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

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

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

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

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

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

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

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

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
	kznf__ZNF613_Imbeault2017_RP_RCADE	5.97	0.16	ZNF613 (directAnnotation).	B cells
	jaspar__MA1125.1	5.87	0.158	ZNF384 (directAnnotation).	B cells
	transfac_pro__M01250	5.02	0.138	E2F1 (directAnnotation).	B cells
	transfac_public__M00415	4.85	0.135	ZEB1 (directAnnotation).	B cells
	tfdimers__MD00187	4.58	0.129	GATA1; GATA2; GATA3; GATA4; GATA5; GATA6 (directAnnotation).	B cells
	transfac_pro__M06678	4.43	0.125	ZNF287 (inferredBy_Orthology).	B cells
	taipale_tf_pairs__ELK1_FOXI1_RSCGGAANRWMAACAN_CAP_repr	4.4	0.125	ELK1; FOXI1 (directAnnotation).	B cells
	metacluster_167.5	4.34	0.123	EHF; ELF5; NFATC3; SPI1; SPI1; SPI1; SPI1; SPI1; SPI1; SPI1; SPI1; SPI1; SPI1; SPI1; SPIB; SPIB; SPIB; SPIB; SPIB; SPIB; SPIB; SPIB; SPIB; SPIB; SPIC; SPIC; STAT5A (directAnnotation). ETS1; SPI1; SPI1; SPI1; SPI1; SPI1; SPI1; SPIB; SPIC (inferredBy_Orthology).	B cells
	metacluster_130.2	4.15	0.119	ZNF182; ZNF22; ZNF225; ZNF225; ZNF285; ZNF362; ZNF362; ZNF384; ZNF487; ZNF512; ZNF570; ZNF613 (directAnnotation). ZNF384 (inferredBy_Orthology).	B cells
	dbtfbs__GMEB1_K562_ENCSR928KOR_merged_N1	4.15	0.119	GMEB1 (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
	metacluster_2.8	6.11	0.0846	IRF4; IRF5; IRF6; IRF9 (directAnnotation). IRF3; IRF5; IRF5; IRF6 (inferredBy_Orthology).	B cells
	metacluster_2.9	4.65	0.0704	IRF2; IRF2; IRF2; PRDM1; PRDM1 (directAnnotation). PRDM1 (inferredBy_Orthology).	B cells
	jaspar__MA1952.1	4.48	0.0688	FOXJ2 (directAnnotation).	B cells
	metacluster_2.6	4.02	0.0642	IRF1; IRF1; IRF1; IRF1; IRF1; IRF1; IRF1; IRF1; IRF1; IRF1; IRF2; IRF2; IRF2; IRF2; IRF2; IRF2; IRF2; IRF3; IRF3; IRF3; IRF3; IRF3; IRF3; IRF4; IRF4; IRF4; IRF4; IRF4; IRF5; IRF5; IRF5; IRF5; IRF5; IRF5; IRF5; IRF6; IRF7; IRF7; IRF7; IRF7; IRF7; IRF7; IRF7; IRF8; IRF8; IRF8; IRF8; IRF8; IRF8; IRF8; IRF8; IRF9; IRF9; IRF9; IRF9; IRF9; IRF9; IRF9; STAT1; STAT2; STAT2; STAT2; STAT2; ZNF426; ZNF71 (directAnnotation). IRF1; IRF1; IRF3; IRF8 (inferredBy_Orthology).	B cells
	metacluster_113.4	4.01	0.0642	MYB; MYB; MYBL1; MYBL2 (directAnnotation). MYB; MYB; MYBL1; MYBL2 (inferredBy_Orthology).	B cells
	jaspar__MA0776.1	3.95	0.0636	MYBL1 (directAnnotation).	B cells
	transfac_pro__M05803	3.75	0.0616	ZNF584 (directAnnotation).	B cells
	metacluster_22.21	3.6	0.0601	NFE2L2 (inferredBy_Orthology).	B cells
	tfdimers__MD00007	3.56	0.0598	E2F1; IRF8 (directAnnotation).	B cells
	tfdimers__MD00138	3.54	0.0595	IRF1; IRF2; IRF3; IRF4; IRF5; IRF7; IRF8; IRF9; MYB (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
IRF7	metacluster_2.6	down	B cells	post
STAT1	metacluster_2.6	down	B cells	post
STAT2	metacluster_2.6	down	B cells	post
IRF7	tfdimers__MD00138	down	B cells	post
IRF7	metacluster_2.7	down	B cells	post
STAT1	metacluster_2.7	down	B cells	post
STAT2	metacluster_2.7	down	B cells	post
SPIB	metacluster_167.5	down	B cells	post
STAT1	cisbp__M11350	down	B cells	post
STAT1	tfdimers__MD00177	down	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."