DRMref Logo

Home

Download

Statistics

Landscape

Help

Contact

Center for Computational Systems Medicine
leaf

Dataset summary

leaf

Drug summary

leaf

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

leaf

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

leaf

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

leaf

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

Soverview

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

Soverview

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

Soverview

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

Soverview

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

Soverview

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

Soverview

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

     •

Differentially expressed genes act as transcription factors

Dataset: GSE150930

Dataset summary for GSE150930

Datast informationDatasetGSE150930
PMID33194728
Raw data ID/linkPRJNA634108
OrganismHomo sapiens
Sourcepatients
TissuePeripheral blood mononuclear cells
Cancer type level1Chronic lymphocytic leukemia
Cancer type level2Mucosa-assisted lymphoid tissue (MALT) lymphoma
Regimenrituximab + cyclophosphamide + fludarabine
Drug typeImmunotherapy
Sample sizeresistant 1, sensitive 1
Cell number2630
Extract protocol10x genomics
Data processingCellRanger
Public datePublic on Oct 27, 2020
DescriptionThis dataset has 1 patient with a sensitive pre-treatment sample and a resistant post-treatment sample.

Top

Drug summary for GSE150930

Drug nameDrugBank IDDrug typeTargets nameTargets uniprot ID
"Rituximab"

DB00073

biotechMS4A1P11836
"Cyclophosphamide"

DB00531

small moleculeNR1I2O75469
"Fludarabine"

DB01073

small moleculeDCK; POLA1; RRM1P27707; P09884; P23921

Top

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

Top

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.)

Top

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

Top

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.)

resistant vs. sensitive

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

Top

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

MMS19

ENSG00000155229-0.7369662.78e-064.38e-0200.667Mono/MacroNA

TNFAIP8L1

ENSG00000185361-0.7369662.78e-064.38e-0200.667Mono/MacroNA

AC093495.1

NA-0.7369662.78e-064.38e-0200.667Mono/MacroNA

SLC25A46

ENSG00000164209-0.7369662.78e-064.38e-0200.667Mono/MacroNA

MTURN

ENSG00000180354-0.7369662.78e-064.38e-0200.667Mono/MacroNA

NUDCD1

ENSG00000120526-0.7369662.78e-064.38e-0200.667Mono/MacroNA

ARMH3

ENSG00000120029-0.7369662.78e-064.38e-0200.667Mono/MacroNA

AC063950.1

NA-0.7369662.78e-064.38e-0200.667Mono/MacroNA

LTB

ENSG000002234480.6304661.19e-341.88e-300.6340.374Malignant cellsNA

IGKC

ENSG000002115920.6055140.00e+000.00e+0010.998Malignant cellsNA

SYNE2

ENSG000000546540.5861985.19e-338.20e-290.6260.397Malignant cellsNA

B2M

ENSG000002736860.5063510.00e+000.00e+0011Malignant cellsNA

HLA-B

ENSG000002064500.4881813.92e-446.30e-400.9890.975Malignant cellsNA

IGHM

ENSG000002826570.4470325.50e-328.69e-280.9930.975Malignant cellsNA

TMSB10

ENSG000000345100.4450188.83e-441.39e-390.9950.995Malignant cellsNA

RPLP1

ENSG000001378180.4182110.00e+001.12e-4411Malignant cellsNA

DBI

ENSG000001553680.4010431.50e-222.36e-180.9240.835Malignant cellsNA

HLA-C

ENSG000002064350.3945181.75e-232.76e-190.8090.673Malignant cellsNA

CD52

ENSG000001694420.3690512.01e-203.17e-160.940.88Malignant cellsNA

RPL27A

ENSG000001664410.3658911.43e-302.27e-260.9970.992Malignant cellsNA

BIRC3

ENSG000000234450.3605081.07e-161.68e-120.4840.323Malignant cellsNA

DDX5

ENSG000001086540.352055.10e-258.06e-210.9760.938Malignant cellsNA

XIST

ENSG000002298070.3506714.42e-186.99e-140.6890.522Malignant cellsNA

PEBP1

ENSG000000892200.3482341.04e-211.64e-170.7960.638Malignant cellsNA

IRF1

ENSG000001253470.3479891.24e-141.97e-100.4450.295Malignant cellsNA

TPM3

ENSG000001435490.3456823.02e-194.78e-150.7840.639Malignant cellsNA

RPS14

ENSG000001645870.3443753.83e-396.04e-350.9991Malignant cellsNA

RPS12

ENSG000001123060.3425223.29e-365.19e-3211Malignant cellsNA

S100A6

ENSG000001979560.3408781.55e-162.45e-120.7810.645Malignant cellsNA

YWHAZ

ENSG000001649240.3401832.57e-214.06e-170.8310.718Malignant cellsNA

SERF2

ENSG000001402640.3348751.56e-272.46e-230.9830.939Malignant cellsNA

ADTRP

ENSG000001118630.334782.17e-283.43e-240.3370.123Malignant cellsNA

RPS18

ENSG000002233670.3337761.26e-341.99e-300.9991Malignant cellsNA

ARPC1B

ENSG000001304290.3243022.45e-213.87e-170.5740.373Malignant cellsNA

STAT1

ENSG000001154150.321782.09e-203.30e-160.2850.118Malignant cellsNA

ATP5F1E

ENSG000001241720.315972.02e-183.19e-140.8770.785Malignant cellsNA

CXXC5

ENSG000001716040.30877.13e-201.13e-150.4780.283Malignant cellsNA

AC103591.3

NA0.3047555.93e-139.37e-090.4920.344Malignant cellsNA

S100A4

ENSG000001961540.3030792.45e-093.88e-050.6160.492Malignant cellsNA

COX4I1

ENSG000001311430.2883772.15e-163.39e-120.830.714Malignant cellsNA

PXDNL

ENSG000001474850.2874195.18e-188.18e-140.3720.197Malignant cellsNA

AC007364.1

NA0.2872026.60e-221.04e-170.2550.088Malignant cellsNA

ATP5MG

ENSG000001672830.2867061.79e-152.84e-110.6440.484Malignant cellsNA

ABCA6

ENSG000001542620.2859928.55e-161.35e-110.650.485Malignant cellsNA

ETS1

ENSG000001349540.281755.82e-179.20e-130.4490.273Malignant cellsNA

ARPC3

ENSG000001112290.2809152.44e-163.85e-120.8340.692Malignant cellsNA

RPL35

ENSG000001369420.2782182.45e-243.87e-200.9940.988Malignant cellsNA

RPL18A

ENSG000001056400.2748853.36e-235.31e-190.9990.999Malignant cellsNA

ISG20

ENSG000001721830.272372.87e-154.53e-110.4540.286Malignant cellsNA

CFLAR

ENSG000000034020.2706721.08e-121.71e-080.5180.374Malignant cellsNA
Page: 1 2 3

Top

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.)

Top

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.)

Top

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
boxplot
MechnismPvalFDRSignatureGenesetOverlapBackgroundCell typeEnriched Genes
Unusual Activation of Pro-survival Pathway1.20e-066.20e-061017811523467Malignant cellsCFLAR,ID1,JUN,PKM,S100A4,YWHAZ,BTG1,DUSP1,DUSP2,EGR1,ETS1,GAPDH,LDHA,PGK1,ENO1
Epigenetic Alteration of DNA, RNA or Protein8.60e-011.00e+00101455123467Malignant cellsGAPDH
Aberration of the Drug's Therapeutic Target1.00e+001.00e+0010190023467Malignant cells
Drug Inactivation by Structure Modification1.00e+001.00e+0010127023467Malignant cells
Irregularity in Drug Uptake and Drug Efflux1.00e+001.00e+0010137023467Malignant cells

Enrichment results for 1 known drug resistance mechanisms in TME cells

boxplot
MechnismPvalFDRSignatureGenesetOverlapBackgroundCell typeEnriched Genes
Regulation by the Disease Microenvironment1.00e+001.00e+002186023467CD4+ T cellsNA
Regulation by the Disease Microenvironment1.00e+001.00e+008186023467Mono_MacroNA

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

boxplot

boxplot

boxplot

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

boxplot

boxplot

boxplot

Top

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
boxplotboxplot

Top

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
motifmetacluster_82.44.980.119ZFP30 (directAnnotation). Malignant cells
motiftransfac_pro__M063664.540.111ZNF530 (directAnnotation). Malignant cells
motifmetacluster_9.114.20.104GBX2 (directAnnotation). Malignant cells
motiftaipale_tf_pairs__TEAD4_SPIB_RGAATGCGGAAGTN_CAP_24.040.101SPIB; TEAD4 (directAnnotation). Malignant cells
motifmetacluster_12.13.840.0977ZNF3 (directAnnotation). Malignant cells
motifmetacluster_2.93.820.0972IRF2; IRF2; IRF2; PRDM1; PRDM1 (directAnnotation). PRDM1 (inferredBy_Orthology). Malignant cells
motiftaipale_tf_pairs__ERF_MAX_RSCGGAANCACGTGN_CAP_repr3.810.097ERF; MAX (directAnnotation). Malignant cells
motiftaipale_tf_pairs__ETV2_GSC2_RCCGGANNNNNNNNNTAATCCN_CAP_repr3.720.0954ETV2; GSC2 (directAnnotation). Malignant cells
motifjaspar__MA0693.33.70.095VDR (inferredBy_Orthology). Malignant cells
motifhdpi__KLF43.630.0936KLF4 (directAnnotation). Malignant cells
Page: 1 2 3 4 5 6

Motifs and TFs regulating down-regulated DEGs in resistant group
motifmotifNESAUCTF_highConfCell_type
motiftfdimers__MD000518.440.529GABPA; STAT6 (directAnnotation). CD4+ T cells
motifswissregulon__hs__PAX28.30.52PAX2 (directAnnotation). CD4+ T cells
motiftransfac_pro__M058727.940.498ZNF655 (directAnnotation). CD4+ T cells
motifkznf__ZNF432_Imbeault2017_RP_RCADE7.790.489ZNF432 (directAnnotation). CD4+ T cells
motiftransfac_pro__M059317.740.486ZNF556 (directAnnotation). CD4+ T cells
motifhomer__YTKGATAHAGTATTCTWGGTNGGCA_ZNF1367.660.482ZNF136 (directAnnotation). CD4+ T cells
motifmetacluster_44.137.660.481NKX3-1; NKX3-2 (directAnnotation). CD4+ T cells
motiftaipale_tf_pairs__ELK1_FOXI1_RSCGGAANRTMAAYA_CAP_repr7.450.468ELK1; FOXI1 (directAnnotation). CD4+ T cells
motifjaspar__MA1962.17.420.467SOX2 (directAnnotation). CD4+ T cells
motiftfdimers__MD004727.420.467EP300; HOXA13 (directAnnotation). CD4+ T cells
Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41

Top

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

IRF1

metacluster_2.7upMalignant cellsNA

STAT1

metacluster_2.7upMalignant cellsNA

IRF1

tfdimers__MD00527upMalignant cellsNA

NR4A1

hdpi__NR4A1downMalignant cellsNA
Page: 1




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."