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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: GSE197268_Axi-cel

Dataset summary for GSE197268_Axi-cel

Datast information	Dataset	GSE197268_Axi-cel
	PMID	36097221
	Raw data ID/link	phs002922.v1.p1
	Organism	Homo sapiens
	Source	patients
	Tissue	Peripheral blood mononuclear cells
	Cancer type level1	Acute lymphoblastic leukemia
	Cancer type level2	Large B-cell acute lymphoblastic leukemia (B-ALL)
	Regimen	axi-cel (CAR-T)
	Drug type	Immunotherapy
	Sample size	pre (resistant 4, sensitive 6); post (resistant 7, sensitive 9)
	Cell number	121362
	Extract protocol	10x genomics
	Data processing	CellRanger 6.0.1
	Public date	Public on Jul 13, 2022
	Description	This dataset has 16 patients, 10 of whom have both pre- and post-treatment samples.

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Drug summary for GSE197268_Axi-cel

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"axi-cel (CAR-T)" 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.)

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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
MT-RNR2	ENSG00000210082	0.283273	0.00e+00	0.00e+00	1	1	NK cells	pre
RPS21	ENSG00000171858	0.282708	0.00e+00	0.00e+00	0.988	0.973	NK cells	pre
MT-CO3	ENSG00000198938	0.280471	0.00e+00	0.00e+00	0.999	0.997	NK cells	pre
PLAC8	ENSG00000145287	0.27957	0.00e+00	0.00e+00	0.635	0.453	NK cells	pre
EIF3G	ENSG00000130811	0.27843	0.00e+00	1.82e-44	0.738	0.61	NK cells	pre
GZMA	ENSG00000145649	0.278027	0.00e+00	0.00e+00	0.944	0.877	NK cells	pre
RPL37	ENSG00000145592	0.277288	0.00e+00	0.00e+00	0.996	0.992	NK cells	pre
CD300A	ENSG00000167851	0.275577	0.00e+00	0.00e+00	0.532	0.352	NK cells	pre
TRBC1	ENSG00000281981	0.27245	0.00e+00	1.57e-43	0.696	0.541	NK cells	pre
XCL2	ENSG00000143185	0.272439	1.98e-35	4.90e-31	0.259	0.158	NK cells	pre
GZMH	ENSG00000100450	0.272012	2.62e-33	6.50e-29	0.809	0.737	NK cells	pre
BTN3A2	ENSG00000186470	0.269135	0.00e+00	0.00e+00	0.44	0.264	NK cells	pre
TMSB4X	ENSG00000205542	0.267151	0.00e+00	0.00e+00	0.998	0.999	NK cells	pre
MT-RNR1	ENSG00000211459	0.267134	1.96e-44	4.97e-40	0.999	0.996	NK cells	pre
RPL38	ENSG00000172809	0.265392	0.00e+00	0.00e+00	0.873	0.799	NK cells	pre
MT-ND4L	ENSG00000212907	0.264321	0.00e+00	0.00e+00	0.994	0.973	NK cells	pre
MT-ND1	ENSG00000198888	0.261759	0.00e+00	0.00e+00	0.997	0.973	NK cells	pre
SPN	ENSG00000197471	0.260284	0.00e+00	0.00e+00	0.701	0.538	NK cells	pre
MT-ND2	ENSG00000198763	0.257423	0.00e+00	0.00e+00	0.958	0.9	NK cells	pre
TMA7	ENSG00000232112	0.257381	0.00e+00	0.00e+00	0.849	0.74	NK cells	pre
TCF25	ENSG00000141002	0.255822	0.00e+00	1.66e-41	0.632	0.472	NK cells	pre
C12orf75	ENSG00000235162	0.255718	3.27e-43	8.10e-39	0.574	0.429	NK cells	pre
CYBA	ENSG00000051523	0.255315	0.00e+00	0.00e+00	0.99	0.976	NK cells	pre
GIMAP4	ENSG00000133574	0.254523	1.03e-42	2.55e-38	0.678	0.542	NK cells	pre
CD63	ENSG00000135404	0.254467	0.00e+00	7.01e-45	0.749	0.614	NK cells	pre
LAIR1	ENSG00000276163	0.253932	0.00e+00	0.00e+00	0.331	0.17	NK cells	pre
TRAF3IP3	ENSG00000009790	0.252686	5.61e-45	1.31e-40	0.718	0.582	NK cells	pre
CALM1	ENSG00000198668	0.250824	0.00e+00	0.00e+00	0.993	0.978	NK cells	pre
FBXO7	ENSG00000100225	-0.27122	7.83e-25	1.94e-20	0.284	0.363	NK cells	pre
MKRN1	ENSG00000133606	-0.275181	5.45e-29	1.35e-24	0.196	0.286	NK cells	pre
CD3D	ENSG00000167286	-0.2821	1.61e-43	3.99e-39	0.172	0.307	NK cells	pre
COTL1	ENSG00000103187	-0.29761	0.00e+00	0.00e+00	0.314	0.502	NK cells	pre
BCL2L1	ENSG00000171552	-0.320633	1.69e-36	4.18e-32	0.214	0.316	NK cells	pre
LGALS3	ENSG00000131981	-0.326771	1.28e-28	3.17e-24	0.175	0.261	NK cells	pre
RPS4Y1	ENSG00000129824	-0.331511	0.00e+00	0.00e+00	0.487	0.726	NK cells	pre
ADIPOR1	ENSG00000159346	-0.358243	0.00e+00	0.00e+00	0.192	0.322	NK cells	pre
GYPC	ENSG00000136732	-0.360074	2.10e-44	5.34e-40	0.481	0.569	NK cells	pre
UBB	ENSG00000170315	-0.431589	0.00e+00	0.00e+00	0.878	0.912	NK cells	pre
BNIP3L	ENSG00000104765	-0.450529	0.00e+00	0.00e+00	0.173	0.303	NK cells	pre
FKBP8	ENSG00000105701	-0.45289	0.00e+00	0.00e+00	0.509	0.599	NK cells	pre
GPX1	ENSG00000233276	-0.452951	0.00e+00	0.00e+00	0.406	0.609	NK cells	pre
YBX3	ENSG00000060138	-0.539449	0.00e+00	0.00e+00	0.069	0.258	NK cells	pre
SNCA	ENSG00000145335	-0.686771	0.00e+00	0.00e+00	0.047	0.263	NK cells	pre
SLC25A39	ENSG00000013306	-0.815262	0.00e+00	0.00e+00	0.231	0.417	NK cells	pre
SLC25A37	ENSG00000147454	-0.948293	0.00e+00	0.00e+00	0.074	0.318	NK cells	pre
ALAS2	ENSG00000158578	-1.15568	0.00e+00	0.00e+00	0.029	0.296	NK cells	pre
HBD	ENSG00000223609	-1.21029	0.00e+00	0.00e+00	0.018	0.252	NK cells	pre
HBA1	ENSG00000206172	-1.78432	0.00e+00	0.00e+00	0.041	0.378	NK cells	pre
HBA2	ENSG00000188536	-1.94933	0.00e+00	0.00e+00	0.036	0.369	NK cells	pre
HBB	ENSG00000244734	-2.93916	0.00e+00	0.00e+00	0.056	0.432	NK 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
IRF1	ENSG00000125347	1.06567	7.51e-09	1.86e-04	0.828	0.463	Progenitors	post
JUND	ENSG00000130522	1.06284	8.25e-12	2.05e-07	1	0.89	Progenitors	post
H1-10	ENSG00000184897	0.947586	2.93e-07	7.27e-03	0.92	0.756	Progenitors	post
CD52	ENSG00000169442	0.90959	9.81e-09	2.43e-04	0.77	0.378	Progenitors	post
HLA-A	ENSG00000227715	0.825301	1.04e-15	2.57e-11	1	0.988	Progenitors	post
XIST	ENSG00000229807	0.756729	2.41e-14	5.97e-10	0.529	0	Progenitors	post
HLA-DRB5	ENSG00000198502	0.734036	9.11e-07	2.26e-02	0.828	0.561	Progenitors	post
RPS4X	ENSG00000198034	0.714503	9.03e-17	2.24e-12	1	1	Progenitors	post
HLA-E	ENSG00000206493	0.615846	4.19e-08	1.04e-03	0.977	0.744	Progenitors	post
UBC	ENSG00000150991	0.611962	3.74e-09	9.26e-05	1	0.829	Progenitors	post
HLA-C	ENSG00000206435	0.597232	4.10e-09	1.02e-04	1	0.976	Progenitors	post
H3-3B	ENSG00000132475	0.596022	6.15e-08	1.52e-03	1	0.988	Progenitors	post
H2AC6	ENSG00000180573	0.499571	1.76e-06	4.35e-02	0.506	0.159	Progenitors	post
EIF1	ENSG00000173812	0.442785	1.52e-09	3.75e-05	1	0.988	Progenitors	post
TPT1	ENSG00000133112	0.408435	6.96e-07	1.73e-02	1	1	Progenitors	post
ACCS	ENSG00000110455	0.407207	4.29e-07	1.06e-02	0.368	0.049	Progenitors	post
RPS27	ENSG00000177954	0.393913	1.49e-07	3.68e-03	1	1	Progenitors	post
RPS14	ENSG00000164587	-0.339315	8.76e-07	2.17e-02	1	1	Progenitors	post
TXLNGY	ENSG00000131002	-0.417013	2.89e-07	7.15e-03	0.023	0.317	Progenitors	post
RPL23A	ENSG00000198242	-0.431499	4.50e-07	1.12e-02	0.931	0.951	Progenitors	post
MYC	ENSG00000136997	-0.460431	1.26e-06	3.12e-02	0.126	0.463	Progenitors	post
PHB2	ENSG00000215021	-0.466641	1.99e-06	4.94e-02	0.609	0.854	Progenitors	post
RAN	ENSG00000132341	-0.552685	2.22e-07	5.49e-03	0.655	0.902	Progenitors	post
NME2	ENSG00000243678	-0.565001	1.51e-08	3.74e-04	0.46	0.866	Progenitors	post
MT-CO1	ENSG00000198804	-0.626147	1.64e-09	4.08e-05	1	1	Progenitors	post
SLC25A3	ENSG00000075415	-0.651917	7.60e-09	1.88e-04	0.805	0.951	Progenitors	post
ACTG1	ENSG00000184009	-0.654849	6.17e-08	1.53e-03	0.977	1	Progenitors	post
MT-CO3	ENSG00000198938	-0.702116	2.41e-09	5.97e-05	1	0.988	Progenitors	post
GAPDH	ENSG00000111640	-0.711166	1.76e-09	4.37e-05	1	1	Progenitors	post
RBM3	ENSG00000102317	-0.838409	1.15e-08	2.84e-04	0.494	0.756	Progenitors	post
RPS4Y1	ENSG00000129824	-1.7218	5.60e-27	1.39e-22	0.046	0.939	Progenitors	post
MPO	ENSG00000005381	-2.73264	3.04e-08	7.53e-04	0.034	0.378	Progenitors	post
RPL37A	ENSG00000197756	0.473377	1.99e-06	4.93e-02	1	1	pDCs	post
IFI44L	ENSG00000137959	-0.694995	1.78e-07	4.42e-03	0.092	0.467	pDCs	post
GZMB	ENSG00000100453	0.579561	0.00e+00	6.03e-44	0.982	0.975	NK cells	post
CLIC3	ENSG00000169583	0.484134	1.75e-23	4.34e-19	0.71	0.579	NK cells	post
RPS26	ENSG00000197728	0.483976	7.43e-44	1.85e-39	0.955	0.9	NK cells	post
LAIR2	ENSG00000274084	0.435528	1.15e-27	2.84e-23	0.4	0.233	NK cells	post
H4C3	ENSG00000197061	0.406638	3.14e-09	7.77e-05	0.566	0.471	NK cells	post
CAPG	ENSG00000042493	0.345024	1.59e-14	3.93e-10	0.278	0.171	NK cells	post
FCER1G	ENSG00000158869	0.336257	3.00e-22	7.44e-18	0.813	0.709	NK cells	post
FOS	ENSG00000170345	0.327323	2.62e-07	6.48e-03	0.443	0.36	NK cells	post
HSP90AA1	ENSG00000080824	0.305092	7.63e-15	1.89e-10	0.954	0.927	NK cells	post
CMC1	ENSG00000187118	0.291241	9.24e-18	2.29e-13	0.63	0.482	NK cells	post
TCF25	ENSG00000141002	0.288461	2.26e-10	5.61e-06	0.657	0.602	NK cells	post
HSPA5	ENSG00000044574	0.269852	1.09e-09	2.71e-05	0.725	0.641	NK cells	post
KLRC1	ENSG00000134545	0.261198	1.04e-18	2.57e-14	0.709	0.53	NK cells	post
ISG15	ENSG00000187608	-0.261984	2.16e-08	5.35e-04	0.583	0.642	NK cells	post
MALAT1	ENSG00000251562	-0.293105	5.84e-15	1.45e-10	0.997	0.999	NK cells	post
ITM2A	ENSG00000078596	-0.294733	6.16e-14	1.53e-09	0.253	0.362	NK 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	5.00e-02	5.00e-02	45	186	2	23467	CD4+ T cells	BCL2,CXCR4
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	42	186	0	23467	CD8+ T cells	NA
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	22	186	0	23467	cDCs	NA
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	57	186	0	23467	Mono_Macro	NA
Regulation by the Disease Microenvironment	5.20e-01	5.20e-01	93	186	1	23467	NK cells	BCL2L1
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	7	186	0	23467	pDCs	NA

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	4.90e-02	4.90e-02	103	186	3	23467	CD4+ T cells	TGFB1,CXCR4,MALAT1
Regulation by the Disease Microenvironment	7.10e-02	7.10e-02	196	186	4	23467	CD8+ T cells	PARP1,GATA3,HNRNPA2B1,MALAT1
Regulation by the Disease Microenvironment	5.20e-01	5.20e-01	91	186	1	23467	cDCs	TGFB1
Regulation by the Disease Microenvironment	2.40e-01	2.40e-01	117	186	2	23467	Mono_Macro	HNRNPA2B1,MALAT1
Regulation by the Disease Microenvironment	1.50e-01	1.50e-01	20	186	1	23467	NK cells	MALAT1
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	2	186	0	23467	pDCs	NA
Regulation by the Disease Microenvironment	2.20e-01	2.20e-01	32	186	1	23467	Progenitors	MYC

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__M01237	5.17	0.16	TERF1 (directAnnotation).	CD4+ T cells
	transfac_public__M00415	4.75	0.149	ZEB1 (directAnnotation).	CD4+ T cells
	transfac_pro__M06881	4.6	0.145	ZNF549 (directAnnotation).	CD4+ T cells
	metacluster_52.10	4.56	0.144	GTF3C2; ZNF436 (directAnnotation).	CD4+ T cells
	transfac_pro__M06528	4.51	0.143	ZNF527 (directAnnotation).	CD4+ T cells
	transfac_pro__M06458	4.37	0.139	ZNF441 (directAnnotation).	CD4+ T cells
	taipale_tf_pairs__GCM1_FIGLA_CAGCTGNNNNNNNNNNNTGCGGG_CAP	4.35	0.139	FIGLA; GCM1 (directAnnotation).	CD4+ T cells
	transfac_pro__M01665	4.21	0.135	IRF8 (directAnnotation).	CD4+ T cells
	transfac_pro__M12458	4.1	0.132	PRDM4 (directAnnotation).	CD4+ T cells
	transfac_pro__M05626	4.02	0.13	ZNF780A (directAnnotation).	CD4+ T 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
	c2h2_zfs__M0385	5.8	0.205	MTF1 (inferredBy_Orthology).	CD4+ T cells
	homer__GGAAATTCCC_NFkB-p65-Rel	5.31	0.189	RELA (inferredBy_Orthology).	CD4+ T cells
	jaspar__MA1945.1	5	0.18	FIGLA (directAnnotation).	CD4+ T cells
	metacluster_172.16	4.63	0.168	ZNF48 (directAnnotation). ZNF48 (inferredBy_Orthology).	CD4+ T cells
	transfac_pro__M05815	4.59	0.167	ZNF613 (directAnnotation).	CD4+ T cells
	taipale_tf_pairs__MYCL2_SCACGTGS_HT	4.5	0.164	MYCLP1 (directAnnotation).	CD4+ T cells
	transfac_pro__M06493	4.46	0.163	ZNF668 (inferredBy_Orthology).	CD4+ T cells
	transfac_pro__M06990	4.46	0.163	ZNF236 (directAnnotation).	CD4+ T cells
	taipale_tf_pairs__GCM1_SOX2_RTRSGGGNNNATTGTKY_CAP_repr	4.43	0.162	GCM1; SOX2 (directAnnotation).	CD4+ T cells
	cisbp__M07803	4.34	0.159	MYC (directAnnotation).	CD4+ T 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
	taipale_tf_pairs__FLI1_DLX2_RSCGGAARYAATTA_CAP	4.75	0.115	DLX2; FLI1 (directAnnotation).	CD4+ T cells
	metacluster_132.4	4.47	0.11	MEF2B; MEF2B; MEF2B; MEF2B; MEF2C; MEF2C; MEF2D; MEF2D; SRF; SRF; SRF; SRF; SRF; SRF; SRF; SRF; SRF; SRF; SRF; SRF; SRF; SRF; SRF; SRF; SRF; SRF; SRF; SRF; SRF; SRF; SRF (directAnnotation). SRF; SRF; SRF; SRF (inferredBy_Orthology).	CD4+ T cells
	jaspar__MA1657.1	4.16	0.104	ZNF652 (directAnnotation).	CD4+ T cells
	hdpi__ZNF695	3.76	0.0964	ZNF695 (directAnnotation).	CD4+ T cells
	jaspar__MA1483.2	3.76	0.0964	ELF2 (directAnnotation).	CD4+ T cells
	tfdimers__MD00572	3.74	0.096	CEBPA; CEBPB; CEBPD; CEBPE; CEBPG; ZNF333 (directAnnotation).	CD4+ T cells
	metacluster_191.1	3.73	0.096	ZNF528; ZNF528; ZNF528 (directAnnotation).	CD4+ T cells
	metacluster_69.2	3.64	0.0942	DMRT1; DMRT1 (directAnnotation). DMRTB1; DMRTB1 (inferredBy_Orthology).	CD4+ T cells
	metacluster_47.1	3.61	0.0937	E4F1; SPDEF; SPDEF (directAnnotation).	CD4+ T cells
	tfdimers__MD00421	3.55	0.0926	ELF3; POU5F1 (directAnnotation).	CD4+ T 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_44.20	5.32	0.131	NKX3-1 (directAnnotation).	CD4+ T cells
	metacluster_31.3	4.96	0.124	ZSCAN20; ZSCAN29 (directAnnotation).	CD4+ T cells
	tfdimers__MD00399	4.83	0.121	ELF5; NFATC3 (directAnnotation).	CD4+ T cells
	metacluster_44.18	4.64	0.117	NKX3-2 (directAnnotation).	CD4+ T cells
	transfac_pro__M01969	4.59	0.116	FOXO1 (directAnnotation).	CD4+ T cells
	metacluster_44.21	4.57	0.115	NKX3-2 (directAnnotation).	CD4+ T cells
	metacluster_44.13	4.44	0.112	NKX3-1; NKX3-2 (directAnnotation).	CD4+ T cells
	tfdimers__MD00187	4.41	0.112	GATA1; GATA2; GATA3; GATA4; GATA5; GATA6 (directAnnotation).	CD4+ T cells
	transfac_pro__M05768	4.36	0.111	ZNF544 (directAnnotation).	CD4+ T cells
	transfac_pro__M05997	4.27	0.109	ZFP64 (directAnnotation).	CD4+ T 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
JUN	cisbp__M01816	up	CD4+ T cells	post
FOSB	metacluster_111.4	up	cDCs	post
JUN	metacluster_111.4	up	cDCs	post
JUNB	metacluster_111.4	up	cDCs	post
FOS	metacluster_111.4	up	cDCs	post
JUN	metacluster_180.3	up	cDCs	post
IRF7	metacluster_2.6	down	cDCs	post
IRF7	metacluster_2.7	down	cDCs	post
IRF1	metacluster_2.6	down	Mono/Macro	post
STAT1	metacluster_2.6	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."