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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_PacBlood

Dataset summary for GSE169246_PacBlood

Datast information	Dataset	GSE169246_PacBlood
	PMID	34653365
	Raw data ID/link	NA
	Organism	Homo sapiens
	Source	patients
	Tissue	Peripheral blood mononuclear cells
	Cancer type level1	Breast cancer
	Cancer type level2	Advanced triple-negative breast cancer (TNBC)
	Regimen	paclitaxel
	Drug type	Chemotherapy
	Sample size	pre (resistant 4, sensitive 5); post (resistant 4, sensitive 5)
	Cell number	120823
	Extract protocol	10x genomics
	Data processing	CellRanger 3.0.0
	Public date	Public on Sep 15, 2021
	Description	This dataset has 9 patients with both pre -and post-treatment samples.

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Drug summary for GSE169246_PacBlood

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"Paclitaxel"	DB01229	small molecule	TUBB1; BCL2; MAP4; MAP2; MAPT; NR1I2	Q9H4B7; P10415; P27816; P11137; P10636; O75469

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Umap of single cell types and conditions (resistant and sensitive)

Umap of cell types and conditions (resistant and sensitive). If this dataset has both pre-treatment and post-treatment samples, the cell types were annotated together. If this dataset is a cell line dataset, the UMAP of cell clusters and the cell ratio of drug-resistant and sensitive groups within each cluster will also be shown. (If the image exists, the user can click on it to enlarge it in a new window.)

Umap of cell types

Umap of conditions

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Comparison of cell composition between the resistant and sensitive groups

In the pre-treatment samples, the cell composition of the resistant and sensitive groups were compared.
* represents significant difference. (If the image exists, the user can click on it to enlarge it in a new window.)

In the post-treatment samples, the cell composition of the resistant and sensitive groups were compared.
* represents significant difference. (If the image exists, the user can click on it to enlarge it in a new window.)

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Comparison of ITH and EMT scores of malignant cells between the resistant and sensitive groups

Comparison of ITH (intra-tumoral heterogeneity) and EMT (epithelial-mesenchymal transition) scores of malignant cells between the resistant and sensitive groups. ITH represents intratumoral heterogeneity, EMT represents epithelial mesenchymal transition, pre represents pre-treatment, post represents post-treatment, post2 represents longer post-treatment. (If the image exists, the user can click on it to enlarge it in a new window.)

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

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

resistant vs. sensitive

Dot plot of significant ligand-receptor pairs in the resistant group	Dot plot of significant ligand-receptor pairs in the sensitive group

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

resistant vs. sensitive

Dot plot of significant ligand-receptor pairs in the resistant group	Dot plot of significant ligand-receptor pairs in the sensitive group

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

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Differentially expressed genes (DEGs) between the resistant and sensitive groups for each cell type

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

Gene symbol	Gene id	avg_log2FC	p_val	p_val_adj	pct.1	pct.2	Cell type	Timepoint
CAST	ENSG00000153113	0.301962	0.00e+00	1.54e-44	0.492	0.329	B cells	pre
ARHGAP45	ENSG00000180448	0.301183	0.00e+00	0.00e+00	0.377	0.192	B cells	pre
PAPOLA	ENSG00000090060	0.299756	0.00e+00	0.00e+00	0.449	0.292	B cells	pre
POU2AF1	ENSG00000110777	0.299433	0.00e+00	0.00e+00	0.483	0.317	B cells	pre
TUBA1B	ENSG00000123416	0.299089	0.00e+00	0.00e+00	0.478	0.29	B cells	pre
CD47	ENSG00000196776	0.298877	0.00e+00	2.19e-43	0.508	0.349	B cells	pre
CD164	ENSG00000135535	0.298844	0.00e+00	0.00e+00	0.427	0.254	B cells	pre
ELOVL5	ENSG00000012660	0.296232	0.00e+00	1.11e-42	0.497	0.341	B cells	pre
HLA-B	ENSG00000206450	0.295625	0.00e+00	0.00e+00	0.999	0.998	B cells	pre
RNASE6	ENSG00000169413	0.295482	3.50e-44	6.91e-40	0.369	0.227	B cells	pre
IFT57	ENSG00000114446	0.295188	0.00e+00	0.00e+00	0.355	0.195	B cells	pre
GGNBP2	ENSG00000275099	0.294378	0.00e+00	0.00e+00	0.36	0.174	B cells	pre
EPB41	ENSG00000159023	0.29376	0.00e+00	0.00e+00	0.37	0.206	B cells	pre
APBB1IP	ENSG00000077420	0.290642	0.00e+00	4.20e-45	0.48	0.316	B cells	pre
PTBP3	ENSG00000119314	0.290309	5.61e-45	1.23e-40	0.351	0.209	B cells	pre
RAD21	ENSG00000164754	0.289994	0.00e+00	0.00e+00	0.434	0.255	B cells	pre
MEF2A	ENSG00000068305	0.289007	0.00e+00	0.00e+00	0.373	0.214	B cells	pre
TNFAIP8	ENSG00000145779	0.288667	0.00e+00	1.74e-43	0.57	0.413	B cells	pre
ZC3HAV1	ENSG00000105939	0.288091	0.00e+00	0.00e+00	0.348	0.193	B cells	pre
SNRNP70	ENSG00000104852	0.28744	0.00e+00	1.84e-42	0.334	0.189	B cells	pre
TNFRSF13C	ENSG00000159958	0.287226	3.87e-41	7.63e-37	0.524	0.372	B cells	pre
JUNB	ENSG00000171223	0.286103	0.00e+00	2.37e-43	0.378	0.213	B cells	pre
TAF15	ENSG00000276833	0.28596	0.00e+00	0.00e+00	0.393	0.216	B cells	pre
MT-CO1	ENSG00000198804	0.285669	0.00e+00	0.00e+00	1	1	B cells	pre
ARHGEF1	ENSG00000076928	0.285519	0.00e+00	3.08e-44	0.402	0.246	B cells	pre
ZEB2	ENSG00000169554	0.285239	4.67e-41	9.21e-37	0.353	0.211	B cells	pre
HSP90B1	ENSG00000166598	0.285094	7.75e-39	1.53e-34	0.474	0.33	B cells	pre
CSDE1	ENSG00000009307	0.285027	0.00e+00	0.00e+00	0.502	0.33	B cells	pre
DOCK10	ENSG00000135905	0.284931	0.00e+00	0.00e+00	0.298	0.126	B cells	pre
FGD2	ENSG00000146192	0.284597	1.40e-45	2.99e-41	0.492	0.336	B cells	pre
HNRNPDL	ENSG00000152795	0.284365	0.00e+00	3.78e-44	0.699	0.55	B cells	pre
BRD2	ENSG00000234704	0.282902	0.00e+00	0.00e+00	0.442	0.278	B cells	pre
BCLAF1	ENSG00000029363	0.282465	0.00e+00	3.61e-42	0.42	0.265	B cells	pre
HNRNPA3	ENSG00000170144	0.282212	7.01e-45	1.44e-40	0.544	0.386	B cells	pre
SCAF4	ENSG00000156304	0.282079	0.00e+00	0.00e+00	0.311	0.132	B cells	pre
S100A10	ENSG00000197747	0.280744	0.00e+00	0.00e+00	0.493	0.279	B cells	pre
NFKB1	ENSG00000109320	0.280641	0.00e+00	0.00e+00	0.31	0.132	B cells	pre
WIPF1	ENSG00000115935	0.280584	0.00e+00	0.00e+00	0.402	0.241	B cells	pre
IQSEC1	ENSG00000144711	0.280354	0.00e+00	0.00e+00	0.311	0.161	B cells	pre
SENP6	ENSG00000112701	0.279883	0.00e+00	0.00e+00	0.334	0.167	B cells	pre
GLG1	ENSG00000090863	0.279596	0.00e+00	0.00e+00	0.324	0.152	B cells	pre
PRPF8	ENSG00000274442	0.279022	0.00e+00	6.31e-44	0.388	0.232	B cells	pre
FMNL1	ENSG00000184922	0.278745	0.00e+00	0.00e+00	0.403	0.224	B cells	pre
PRRC2C	ENSG00000117523	0.278637	2.82e-37	5.56e-33	0.568	0.437	B cells	pre
CAPZA1	ENSG00000116489	0.278072	0.00e+00	0.00e+00	0.464	0.291	B cells	pre
FUS	ENSG00000089280	0.277976	1.02e-41	2.01e-37	0.59	0.441	B cells	pre
GGA2	ENSG00000103365	0.27785	8.41e-45	1.70e-40	0.425	0.273	B cells	pre
KMT2E	ENSG00000005483	0.277416	9.96e-36	1.97e-31	0.555	0.428	B cells	pre
MOB1A	ENSG00000114978	0.277332	1.26e-44	2.59e-40	0.472	0.318	B cells	pre
ATRX	ENSG00000085224	0.276991	5.39e-40	1.06e-35	0.466	0.321	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
ACTB	ENSG00000075624	1.02077	5.27e-12	1.04e-07	1	0.955	Progenitors	post
ACTG1	ENSG00000184009	0.927729	9.42e-13	1.86e-08	1	0.951	Progenitors	post
NPM1	ENSG00000181163	0.869728	1.82e-14	3.60e-10	1	0.935	Progenitors	post
HLA-B	ENSG00000206450	0.84451	1.25e-12	2.46e-08	0.98	0.895	Progenitors	post
HNRNPA1	ENSG00000135486	0.829142	1.11e-11	2.19e-07	1	0.923	Progenitors	post
LAPTM4B	ENSG00000104341	0.822856	5.77e-10	1.14e-05	0.804	0.417	Progenitors	post
TUBA1B	ENSG00000123416	0.819877	1.74e-11	3.44e-07	0.843	0.393	Progenitors	post
EEF1A1	ENSG00000156508	0.793986	2.48e-12	4.89e-08	1	1	Progenitors	post
TUBB	ENSG00000235067	0.786445	7.89e-12	1.56e-07	0.922	0.583	Progenitors	post
H3F3B	NA	0.776868	5.98e-11	1.18e-06	0.98	0.737	Progenitors	post
RBM3	ENSG00000102317	0.773442	5.17e-11	1.02e-06	0.824	0.377	Progenitors	post
H2AFY	NA	0.772593	4.42e-12	8.73e-08	0.961	0.721	Progenitors	post
EEF1G	ENSG00000254772	0.762135	2.58e-12	5.09e-08	1	0.887	Progenitors	post
MT-ATP8	ENSG00000228253	0.757504	1.68e-08	3.31e-04	0.98	0.907	Progenitors	post
ZFP36L2	ENSG00000152518	0.752723	3.47e-09	6.85e-05	0.98	0.765	Progenitors	post
HSPA8	ENSG00000109971	0.684539	4.06e-08	8.01e-04	0.843	0.51	Progenitors	post
MT-ND4L	ENSG00000212907	0.683375	1.58e-08	3.12e-04	0.98	0.972	Progenitors	post
RPL3	ENSG00000100316	0.67673	4.31e-13	8.50e-09	1	1	Progenitors	post
HSP90AB1	ENSG00000096384	0.666922	6.93e-10	1.37e-05	0.98	0.903	Progenitors	post
RHOA	ENSG00000067560	0.663145	5.66e-10	1.12e-05	0.941	0.595	Progenitors	post
LDHB	ENSG00000111716	0.661659	2.23e-10	4.40e-06	1	0.85	Progenitors	post
NFE2	ENSG00000123405	0.657882	3.79e-09	7.48e-05	0.922	0.656	Progenitors	post
APEX1	ENSG00000100823	0.653985	2.84e-08	5.60e-04	0.863	0.615	Progenitors	post
PCBP1	ENSG00000169564	0.651123	2.45e-11	4.84e-07	0.824	0.372	Progenitors	post
SLC25A3	ENSG00000075415	0.64739	3.66e-10	7.22e-06	0.961	0.579	Progenitors	post
ATP5F1B	ENSG00000110955	0.642999	6.61e-10	1.31e-05	0.882	0.526	Progenitors	post
CITED2	ENSG00000164442	0.638512	2.48e-09	4.90e-05	0.569	0.182	Progenitors	post
ANP32B	ENSG00000136938	0.628867	3.04e-09	5.99e-05	0.941	0.761	Progenitors	post
EIF3L	ENSG00000100129	0.607148	2.76e-08	5.45e-04	1	0.717	Progenitors	post
PTMA	ENSG00000187514	0.604823	1.48e-11	2.91e-07	1	1	Progenitors	post
SET	ENSG00000119335	0.586183	2.56e-08	5.05e-04	0.882	0.583	Progenitors	post
SARAF	ENSG00000133872	0.584337	1.96e-08	3.88e-04	0.804	0.437	Progenitors	post
PAIP2	ENSG00000120727	0.580796	9.39e-09	1.85e-04	0.725	0.344	Progenitors	post
PEBP1	ENSG00000089220	0.56687	6.35e-09	1.25e-04	0.922	0.599	Progenitors	post
SRP9	ENSG00000143742	0.559114	1.83e-08	3.62e-04	0.686	0.291	Progenitors	post
PCBP2	ENSG00000197111	0.558041	6.98e-09	1.38e-04	1	0.874	Progenitors	post
ARHGDIB	ENSG00000111348	0.548551	5.55e-10	1.10e-05	1	0.903	Progenitors	post
CNBP	ENSG00000169714	0.544901	2.31e-08	4.57e-04	0.843	0.462	Progenitors	post
MORF4L1	ENSG00000185787	0.542778	3.02e-07	5.95e-03	0.765	0.441	Progenitors	post
NCL	ENSG00000115053	0.537875	2.42e-06	4.77e-02	0.804	0.502	Progenitors	post
NREP	ENSG00000134986	0.534974	5.04e-08	9.95e-04	0.765	0.381	Progenitors	post
H1FX	NA	0.532433	5.54e-07	1.09e-02	0.745	0.385	Progenitors	post
LDHA	ENSG00000288299	0.531597	2.65e-07	5.22e-03	0.765	0.441	Progenitors	post
IMPDH2	ENSG00000178035	0.529797	3.39e-07	6.69e-03	0.882	0.571	Progenitors	post
CD34	ENSG00000174059	0.52592	2.18e-06	4.30e-02	0.686	0.336	Progenitors	post
RAN	ENSG00000132341	0.521054	2.37e-06	4.68e-02	0.784	0.522	Progenitors	post
CALR	ENSG00000179218	0.516728	5.72e-08	1.13e-03	0.922	0.555	Progenitors	post
PGK1	ENSG00000102144	0.507758	1.93e-09	3.80e-05	0.725	0.291	Progenitors	post
RTRAF	ENSG00000087302	0.502776	6.30e-08	1.24e-03	0.843	0.547	Progenitors	post
SRSF9	ENSG00000111786	0.495059	1.75e-06	3.46e-02	0.725	0.437	Progenitors	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	3.70e-03	3.70e-03	384	186	9	23467	B cells	BCL2,CDKN1B,NFKB1,TGFBR2,ZEB2,PDCD6IP,HNRNPA2B1,VIM,MALAT1
Regulation by the Disease Microenvironment	4.00e-02	4.00e-02	399	186	7	23467	CD4+ T cells	BCL2,CDKN1B,NFKB1,TGFBR2,CXCR4,HNRNPA2B1,MALAT1
Regulation by the Disease Microenvironment	6.10e-01	6.10e-01	257	186	2	23467	CD8+ T cells	CDKN1B,CXCR4
Regulation by the Disease Microenvironment	2.90e-01	2.90e-01	454	186	5	23467	cDCs	NFKB1,TGFBR2,ZEB2,HNRNPA2B1,VIM
Regulation by the Disease Microenvironment	1.40e-01	1.40e-01	442	186	6	23467	Mono_Macro	TGFB1,TGFBR2,ZEB2,HNRNPA2B1,VIM,MALAT1
Regulation by the Disease Microenvironment	1.50e-01	1.50e-01	548	186	7	23467	NK cells	CDKN1B,TGFBR2,ZEB2,CX3CR1,PDCD6IP,HNRNPA2B1,STAT3
Regulation by the Disease Microenvironment	2.10e-01	2.10e-01	199	186	3	23467	pDCs	HNRNPA2B1,SMAD3,TSPYL2
Regulation by the Disease Microenvironment	5.30e-01	5.30e-01	94	186	1	23467	Plasma cells	CDKN1B

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

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

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

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

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

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

Enrichment results for 1 known drug resistance mechanisms in TME cells

Mechnism	Pval	FDR	Signature	Geneset	Overlap	Background	Cell type	Enriched Genes
Regulation by the Disease Microenvironment	3.60e-01	3.60e-01	160	186	2	23467	B cells	HNRNPA2B1,MALAT1
Regulation by the Disease Microenvironment	2.30e-02	2.30e-02	77	186	3	23467	CD4+ T cells	VIM,LDHB,MALAT1
Regulation by the Disease Microenvironment	4.00e-02	4.00e-02	235	186	5	23467	CD8+ T cells	CXCR4,HNRNPA2B1,VIM,LDHB,MALAT1
Regulation by the Disease Microenvironment	5.20e-01	5.20e-01	348	186	3	23467	cDCs	TGFB1,VIM,MALAT1
Regulation by the Disease Microenvironment	5.50e-03	5.50e-03	89	186	4	23467	Mono_Macro	IL1B,RHOB,VIM,MALAT1
Regulation by the Disease Microenvironment	6.30e-01	6.30e-01	123	186	1	23467	NK cells	MALAT1
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	1	186	0	23467	pDCs	NA
Regulation by the Disease Microenvironment	3.90e-01	3.90e-01	169	186	2	23467	Plasma cells	RHOB,MALAT1
Regulation by the Disease Microenvironment	1.50e-01	1.50e-01	88	186	2	23467	Progenitors	LDHB,MALAT1

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
	hdpi__NRL	3.49	0.104	NRL (directAnnotation).	B cells
	flyfactorsurvey__Mad_FlyReg_FBgn0011648	3.41	0.103	SMAD9 (inferredBy_Orthology).	B cells
	cisbp__M00341	3.41	0.103	PAX6 (directAnnotation).	B cells
	cisbp__M00968	3.37	0.102	MTF2 (directAnnotation).	B cells
	metacluster_141.6	3.28	0.1	MZF1; TAF1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY1; YY2; YY2; ZFP42; ZFP42; ZFP42; ZFP42; ZFP42; ZFP42; ZNF597 (directAnnotation). TAF1; TAF1L (inferredBy_Orthology).	B cells
	hdpi__FEZF2	3.27	0.1	FEZF2 (directAnnotation).	B cells
	hocomoco__TYY2_HUMAN.H11MO.0.D	3.26	0.0998	YY2 (directAnnotation).	B cells
	transfac_pro__M07310	3.23	0.0992	SP5 (directAnnotation).	B cells
	metacluster_67.2	3.19	0.0984	ZNF501 (directAnnotation). ACAA1; E2F2; E2F2; E2F3; E2F3; FOXN4 (inferredBy_Orthology).	B cells
	homer__TWVGGTCCGC_HINFP	3.18	0.0983	HINFP (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__M06404	7.69	0.0949	ZNF497 (directAnnotation).	B cells
	swissregulon__hs__ETV6	6.21	0.0788	ETV6 (directAnnotation).	B cells
	metacluster_140.1	4.59	0.0612	BCL11B; BCL11B (directAnnotation).	B cells
	transfac_pro__M05711	4.57	0.061	ZNF37A (directAnnotation).	B cells
	taipale_tf_pairs__GCM1_ETV4_RTGCGGGCGGAAGTR_CAP	4.51	0.0603	ETV4; GCM1 (directAnnotation).	B cells
	cisbp__M02645	4.44	0.0596	ETS1 (directAnnotation).	B cells
	transfac_pro__M04923	4.42	0.0594	ZBTB33 (directAnnotation).	B cells
	taipale_tf_pairs__GCM2_PITX1_RTRCGGGSGATTAN_CAP_repr	4.37	0.0589	GCM2; PITX1 (directAnnotation).	B cells
	transfac_pro__M06322	4.36	0.0588	ZNF181 (directAnnotation).	B cells
	taipale_tf_pairs__ERF_HOXA3_RSCGGAWNNNNNNNYMATTA_CAP_repr	4.33	0.0584	ERF; HOXA3 (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_141.4	7.77	0.136	GLIS2 (directAnnotation).	B cells
	hocomoco__TYY2_HUMAN.H11MO.0.D	6.74	0.122	YY2 (directAnnotation).	B cells
	taipale__YY2_DBD_NNCCGCCATNW_repr	5.87	0.109	YY2 (directAnnotation).	B cells
	transfac_pro__M06259	5.06	0.0982	ZNF91 (directAnnotation).	B cells
	metacluster_141.2	5.05	0.0979	E2F2; E2F3 (directAnnotation).	B cells
	tfdimers__MD00351	4.69	0.093	IRF8; RFX1; RFX2; RFX3; RFX4; RFX5; RFXANK; RFXAP (directAnnotation).	B cells
	flyfactorsurvey__pho_SOLEXA_F1-3	4.63	0.0921	YY1 (inferredBy_Orthology).	B cells
	metacluster_2.8	4.27	0.0872	IRF4; IRF5; IRF6; IRF9 (directAnnotation). IRF3; IRF5; IRF5; IRF6 (inferredBy_Orthology).	B cells
	transfac_pro__M06715	3.64	0.0784	ZNF331 (directAnnotation).	B cells
	stark__RCGCMATTW	3.63	0.0783	YY1 (inferredBy_Orthology).	B cells

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Motifs and TFs regulating down-regulated DEGs in resistant group of the post-treatment samples

motif	motif	NES	AUC	TF_highConf	Cell_type
	swissregulon__hs__ETV6	7.27	0.123	ETV6 (directAnnotation).	B cells
	hdpi__FLI1	7.2	0.122	FLI1 (directAnnotation).	B cells
	metacluster_2.7	6.53	0.111	IRF1; IRF1; IRF2; IRF2; IRF3; IRF4; IRF5; IRF6; IRF7; IRF7; IRF8; IRF8; IRF9; PRDM1; PRDM1; PRDM1; PRDM1; PRDM1; PRDM1; PRDM1; PRDM1; PRDM1; PRDM1; PRDM1; PRDM1; STAT1; STAT1; STAT2 (directAnnotation). PRDM1; PRDM1; PRDM1 (inferredBy_Orthology).	B cells
	metacluster_2.6	5.92	0.102	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
	transfac_pro__M06763	5.43	0.0949	ZNF225 (directAnnotation).	B cells
	transfac_pro__M04887	5.16	0.091	TCF12 (directAnnotation).	B cells
	metacluster_2.8	5	0.0885	IRF4; IRF5; IRF6; IRF9 (directAnnotation). IRF3; IRF5; IRF5; IRF6 (inferredBy_Orthology).	B cells
	metacluster_79.12	4.82	0.0859	ZNF257 (directAnnotation).	B cells
	jaspar__MA1509.1	4.75	0.0847	IRF6 (directAnnotation).	B cells
	metacluster_161.15	4.73	0.0845	NKX3-1 (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
JUNB	metacluster_137.2	up	CD8+ T cells	post
CEBPD	taipale_tf_pairs__ETV2_CEBPD_RSCGGANNTTGCGYAAN_CAP_repr	up	cDCs	post
SPI1	metacluster_167.5	up	cDCs	post
FOS	tfdimers__MD00165	down	Mono/Macro	post
FOSB	tfdimers__MD00165	down	Mono/Macro	post
JUN	tfdimers__MD00165	down	Mono/Macro	post
JUNB	tfdimers__MD00165	down	Mono/Macro	post
JUND	tfdimers__MD00165	down	Mono/Macro	post
CEBPB	taipale_tf_pairs__GCM1_CEBPB_ATRSGGGNNNNTTRCGYAAN_CAP_repr	down	Mono/Macro	post
CEBPB	tfdimers__MD00359	down	Mono/Macro	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."