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Center for Computational Systems Medicine
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Dataset summary

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Drug summary

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

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Comparison of cell composition between the resistant and sensitive groups (This dataset does not contain this module)

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Comparison of intra-tumor heterogeneity (ITH) and epithelial-mesenchymal transition (EMT) scores of malignant cells between the resistant and sensitive groups

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Difference of cell-cell interactions between the resistant and sensitive groups (This dataset does not contain this module)

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Differentially expressed genes (DEGs) 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 (This dataset does not contain this module)

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Mechanism analysis of drug resistance-related DEGs for each cell type in the post-treatment samples (This dataset does not contain this module)

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

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

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

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Differentially expressed genes act as transcription factors

Dataset: GSE140440

Dataset summary for GSE140440

Datast informationDatasetGSE140440
PMID32513898
Raw data ID/linkPRJNA589746
OrganismHomo sapiens
SourceDU145 and PC cell lines
TissueCell line
Cancer type level1Prostate cancer
Cancer type level2Prostate cancer
Regimendocetaxel
Drug typeChemotherapy
Sample sizeresistant 2, sensitive 2
Cell number284
Extract protocolSMART-seq v4
Data processingNA
Public datePublic on Sep 01, 2020
DescriptionThis dataset has 1 cell line with a sensitive pre-treatment sample and a resistant post-treatment sample.

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Drug summary for GSE140440

Drug nameDrugBank IDDrug typeTargets nameTargets uniprot ID
"Docetaxel"

DB01248

small moleculeTUBB1; MAP2; MAP4; MAPT; BCL2; NR1I2Q9H4B7; P11137; P27816; P10636; P10415; O75469

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

check buttonUmap 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 typesboxplotUmap of conditionsboxplot
Umap of cell clustersboxplotCell ratio of drug-resistant and sensitive groups within each clusterboxplot

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Comparison of cell composition between the resistant and sensitive groups

check buttonIn 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.)

check buttonIn 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

check buttonComparison 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 scoresboxplotComparison of EMT scoresboxplot

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

check buttonIn 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.)

check buttonIn 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.)

check buttonThis 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

check buttonIn 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.

check buttonIn 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.

check buttonThis 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.
Gene symbolGene idavg_log2FCp_valp_val_adjpct.1pct.2Cell typeTimepoint

RP11-479G22.8

NA-1.416612.68e-077.50e-030.5070.791Malignant cellsNA

RECQL4

ENSG00000160957-1.416911.64e-074.59e-030.3730.694Malignant cellsNA

RP5-1186N24.3

NA-1.417085.93e-111.66e-060.3730.746Malignant cellsNA

KIF4A

ENSG00000090889-1.418066.24e-111.74e-060.520.813Malignant cellsNA

EXO1

ENSG00000174371-1.420231.58e-094.41e-050.6330.851Malignant cellsNA

RP11-797A18.6

NA-1.420531.02e-092.86e-050.3470.701Malignant cellsNA

CLN6

ENSG00000128973-1.426334.15e-091.16e-040.3670.709Malignant cellsNA

HOTTIP

ENSG00000243766-1.426611.04e-082.90e-040.3530.694Malignant cellsNA

CTC-425O23.5

NA-1.426811.40e-073.91e-030.8730.91Malignant cellsNA

RP11-676J12.4

NA-1.429181.73e-074.83e-030.6870.799Malignant cellsNA

PLEKHA7

ENSG00000166689-1.430881.31e-083.65e-040.3670.694Malignant cellsNA

CTD-2123J17.2

NA-1.43164.77e-071.33e-020.3470.642Malignant cellsNA

E2F2

ENSG00000282899-1.432212.47e-086.90e-040.50.731Malignant cellsNA

BUB1

ENSG00000169679-1.433432.41e-136.74e-090.780.948Malignant cellsNA

GTPBP4

ENSG00000107937-1.4351.48e-204.15e-1611Malignant cellsNA

AP001505.10

NA-1.435994.01e-071.12e-020.5270.776Malignant cellsNA

ALDH3B1

ENSG00000006534-1.44712.71e-107.57e-060.4130.731Malignant cellsNA

SPHK1

ENSG00000176170-1.447831.39e-063.88e-020.4930.754Malignant cellsNA

CENPE

ENSG00000138778-1.448491.40e-103.91e-060.6730.955Malignant cellsNA

PARPBP

ENSG00000185480-1.450471.42e-123.97e-080.6470.933Malignant cellsNA

POLR2L

ENSG00000177700-1.453923.40e-339.51e-2911Malignant cellsNA

PRODH

ENSG00000277196-1.456093.00e-078.38e-030.2470.545Malignant cellsNA

ADNP2

ENSG00000101544-1.460632.98e-078.34e-030.6270.843Malignant cellsNA

KIF20A

ENSG00000112984-1.462012.44e-096.82e-050.60.866Malignant cellsNA

TMEM238

ENSG00000233493-1.462026.76e-111.89e-060.70.888Malignant cellsNA

SIRT7

ENSG00000187531-1.466732.11e-135.89e-090.540.873Malignant cellsNA

PARD3

ENSG00000148498-1.472754.01e-111.12e-060.960.993Malignant cellsNA

RP11-774D14.1

NA-1.474564.95e-091.38e-040.1330.44Malignant cellsNA

RP11-498C9.15

NA-1.478626.52e-131.82e-080.4330.828Malignant cellsNA

RRM2

ENSG00000171848-1.47883.10e-178.67e-130.9130.985Malignant cellsNA

RP11-271C24.3

NA-1.479563.07e-078.58e-030.3870.687Malignant cellsNA

TM4SF20

ENSG00000168955-1.480341.10e-103.08e-060.3730.746Malignant cellsNA

TK1

ENSG00000167900-1.480581.34e-233.75e-190.921Malignant cellsNA

SGOL2

NA-1.481671.21e-103.38e-060.660.903Malignant cellsNA

POMK

ENSG00000185900-1.489341.00e-072.80e-030.3330.612Malignant cellsNA

NEFM

ENSG00000104722-1.491184.92e-111.38e-060.20.582Malignant cellsNA

ARMC3

ENSG00000165309-1.492327.99e-082.23e-030.360.664Malignant cellsNA

ISG20L2

ENSG00000143319-1.492357.87e-132.20e-080.961Malignant cellsNA

RP11-521C22.2

NA-1.496537.61e-102.13e-050.360.716Malignant cellsNA

PDDC1

NA-1.498171.21e-083.38e-040.9730.978Malignant cellsNA

DGKZ

ENSG00000149091-1.499761.91e-105.34e-060.4530.791Malignant cellsNA

YME1L1

ENSG00000136758-1.506415.21e-251.46e-200.9731Malignant cellsNA

SAA1

ENSG00000288411-1.508643.22e-129.01e-080.1730.56Malignant cellsNA

TMEM139

ENSG00000178826-1.509482.21e-076.19e-030.3730.672Malignant cellsNA

TOP2A

ENSG00000131747-1.511073.95e-131.11e-080.880.97Malignant cellsNA

IFI44L

ENSG00000137959-1.514652.31e-086.45e-040.3530.649Malignant cellsNA

NRCAM

ENSG00000091129-1.514712.27e-076.35e-030.20.5Malignant cellsNA

SOD3

ENSG00000109610-1.51733.85e-131.08e-080.340.709Malignant cellsNA

MTPAP

ENSG00000107951-1.521488.63e-112.41e-060.9130.955Malignant cellsNA

CDR2L

ENSG00000109089-1.523811.28e-113.58e-070.6870.918Malignant cellsNA
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Mechanism analysis of drug resistance-related DEGs for each cell type in the pre-treatment samples

check buttonEnrichment 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.)

check buttonHallmark, 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.)

check buttonHallmark, 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

check buttonEnrichment 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.)

check buttonHallmark, 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.)

check buttonHallmark, 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.)

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

check buttonThis 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.)
Enrichment results for 5 known drug resistance mechanisms in malignant cells
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MechnismPvalFDRSignatureGenesetOverlapBackgroundCell typeEnriched Genes
Unusual Activation of Pro-survival Pathway9.80e-064.90e-05235278111623467Malignant cellsADAM9,ANXA2,AREG,BCAT1,BIRC5,BRCA1,CCND2,CDCP1,CDK6,CDKN1A,DNMT1,FAM168A,GSK3B,HOXA13,IGF2BP1,JUN,MAP1LC3B,PARP1,SOCS2,SPRY2,TGFB1,TGFBR2,PBK,TYMS,VEGFA,AAMDC,ADAM22,SLC25A5,AGR2,ANXA1,BCL10,BTG1,BUB1,CBL,CCNA2,CCNB1,CDK1,CCND1,CCNG2,CD44,HSPD1,CLTC,CLU,CUL4B,CYLD,DUSP2,DHFR,E2F2,ENG,ERCC1,ETS1,EZH2,FANCD2,FGFR1,FUS,FZD1,GPER1,GRB2,GCLM,SLC16A3,HMGB2,HMGN5,HSPA8,EIF4A3,IL1B,CXCL8,ING4,ITGA5,ITGB1,KIF11,KLF4,LDHA,MXD4,NF2,MYBL2,MYO10,NOTCH3,PARP8,PDCD4,PLK1,PSMB5,PTPN12,RAD51,RAB22A,RAB27A,RICTOR,RRM1,RRM2,ROCK2,SDC2,SMC4,SNAI2,SRI,STARD10,TERT,TFAM,TMEM54,TOP2B,USP14,USP22,PLAU,ERCC4,YEATS4,PFKFB3,GNAS,HMGCS1,INSIG1,ITGB3,PRKCA,RCN1,SQLE,SPHK1,GGPS1,SAFB2,PDSS1,ACAT2
Irregularity in Drug Uptake and Drug Efflux1.60e-013.60e-01235237623467Malignant cellsABCB1,ABCC2,ABCA10,ABCF2,ABCE1,ABCG1
Drug Inactivation by Structure Modification2.80e-013.60e-01235227423467Malignant cellsGSS,NME1,CMPK1,CYP51A1
Aberration of the Drug's Therapeutic Target2.90e-013.60e-012352901123467Malignant cellsBRCA1,CDK6,DHFR,EZH2,FGFR1,IL1B,JAK1,COMT,DPP4,MAOA,TOP2A
Epigenetic Alteration of DNA, RNA or Protein1.00e+001.00e+0023524552023467Malignant cellsDNMT1,GSK3B,H2AFY,HOXA13,EIF4G2,SPRY2,TYMS,EZH2,CXCL8,PDCD4,SMC4,TIMP1,SNHG1,LINC00261,GDI2,CDK14,CDR1,MX1,LINC00707,RP11-166P13.3


check buttonHallmark, 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.)
Up-regulated HallmarkUp-regulated KEGGUp-regulated GO BP

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check buttonHallmark, 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.)
Down-regulated HallmarkDown-regulated KEGGDown-regulated GO BP

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

check buttonIn 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.)

check buttonIn 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.)

check buttonThis 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.)
Regulating up-regulated DEGs in resistant groupRegulating down-regulated DEGs in resistant group
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Motifs and transcription factors (TFs) regulating drug resistance-related DEGs for each cell type

check buttonIn 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.)

check buttonIn 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.)

check buttonThis 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.)
Motifs and TFs regulating up-regulated DEGs in resistant group
motifmotifNESAUCTF_highConfCell_type
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Differentially expressed genes act as transcription factors

check buttonThis table shows the differentially expressed genes that act as transcription factors. (Complete files can be downloaded from the download section.)
TFmotifExpressionCell typeTimepoint

KLF13

metacluster_195.2upMalignant cellsNA

KLF9

metacluster_195.2upMalignant cellsNA

KLF4

metacluster_195.2upMalignant cellsNA

KLF7

metacluster_195.2upMalignant cellsNA

KLF13

hocomoco__KLF13_HUMAN.H11MO.0.DupMalignant cellsNA

KLF13

transfac_pro__M07461upMalignant cellsNA

KLF4

transfac_pro__M07461upMalignant cellsNA

KLF7

transfac_pro__M07461upMalignant cellsNA

KLF9

transfac_pro__M07461upMalignant cellsNA

KLF7

metacluster_170.2upMalignant cellsNA
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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."