Schematic overview of the cellular and molecular mechanisms involved in the cancer progression, including the proposed cellular and molecular mechanisms in cancer cells trajectory. AT1: alveolar type 1 cells; AT2: alveolar type 2 cells; AAH: atypical adenomatous hyperplasia; AIS: adenocarcinoma in situ; MIA: minimally invasive adenocarcinoma; IA: invasive adenocarcinoma; EMT: epithelial-mesenchymal transition

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Center for Computational Systems Medicine
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Gene summary

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Malignant transformation analysis

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Malignant transformation related pathway analysis

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Cell-cell communication analysis

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Single-cell gene regulatory network inference analysis

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Somatic mutation of malignant transformation related genes

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Related drugs of malignant transformation related genes

Gene: NCBP2

Gene summary for NCBP2

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

NCBP2

Gene ID

22916

Gene namenuclear cap binding protein subunit 2
Gene AliasCBC2
Cytomap3q29
Gene Typeprotein-coding
GO ID

GO:0000184

UniProtAcc

P52298


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Malignant transformation analysis

check button Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells
check button Malignant transformation involving gene list.
Entrez IDSymbolReplicatesSpeciesOrganTissueAdj P-valueLog2FCMalignancy
22916NCBP2LZE2DHumanEsophagusHGIN4.35e-032.30e-010.0642
22916NCBP2LZE2THumanEsophagusESCC1.81e-069.38e-010.082
22916NCBP2LZE4THumanEsophagusESCC1.35e-175.75e-010.0811
22916NCBP2LZE5THumanEsophagusESCC1.33e-021.86e-010.0514
22916NCBP2LZE7THumanEsophagusESCC2.20e-137.03e-010.0667
22916NCBP2LZE8THumanEsophagusESCC9.91e-133.30e-010.067
22916NCBP2LZE20THumanEsophagusESCC4.85e-063.55e-010.0662
22916NCBP2LZE22THumanEsophagusESCC9.12e-066.20e-010.068
22916NCBP2LZE24THumanEsophagusESCC5.55e-217.09e-010.0596
22916NCBP2LZE21THumanEsophagusESCC2.89e-119.51e-010.0655
22916NCBP2LZE6THumanEsophagusESCC5.70e-085.50e-010.0845
22916NCBP2P1T-EHumanEsophagusESCC1.20e-025.95e-010.0875
22916NCBP2P2T-EHumanEsophagusESCC7.01e-801.74e+000.1177
22916NCBP2P4T-EHumanEsophagusESCC2.05e-511.39e+000.1323
22916NCBP2P5T-EHumanEsophagusESCC1.11e-499.76e-010.1327
22916NCBP2P8T-EHumanEsophagusESCC1.11e-296.33e-010.0889
22916NCBP2P9T-EHumanEsophagusESCC2.02e-379.63e-010.1131
22916NCBP2P10T-EHumanEsophagusESCC1.02e-791.37e+000.116
22916NCBP2P11T-EHumanEsophagusESCC4.87e-218.61e-010.1426
22916NCBP2P12T-EHumanEsophagusESCC2.81e-266.89e-010.1122
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
EsophagusThe image shows the transcriptomic changes along malignancy continuum.log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.ESCC: Esophageal squamous cell carcinoma
HGIN: High-grade intraepithelial neoplasias
LGIN: Low-grade intraepithelial neoplasias
LiverThe image shows the transcriptomic changes along malignancy continuum.log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.HCC: Hepatocellular carcinoma
NAFLD: Non-alcoholic fatty liver disease
Oral CavityThe image shows the transcriptomic changes along malignancy continuum.log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.EOLP: Erosive Oral lichen planus
LP: leukoplakia
NEOLP: Non-erosive oral lichen planus
OSCC: Oral squamous cell carcinoma
SkinThe image shows the transcriptomic changes along malignancy continuum.log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.AK: Actinic keratosis
cSCC: Cutaneous squamous cell carcinoma
SCCIS:squamous cell carcinoma in situ
ThyroidThe image shows the transcriptomic changes along malignancy continuum.log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.ATC: Anaplastic thyroid cancer
HT: Hashimoto's thyroiditis
PTC: Papillary thyroid cancer
∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.

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Malignant transformation related pathway analysis

check buttonFind out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer
check button Figure of enriched GO biological processes.
TissueDisease StageEnriched GO biological Processes
ColorectumADGO analysis - Figure of enriched GO biological processes: Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).
ColorectumSERGO analysis - Figure of enriched GO biological processes: Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).
ColorectumMSSGO analysis - Figure of enriched GO biological processes: Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).
ColorectumMSI-HGO analysis - Figure of enriched GO biological processes: Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).
ColorectumFAPGO analysis - Figure of enriched GO biological processes: Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).
∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).
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check button Enriched GO biological processes.
GO IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustCount
GO:000838026EsophagusHGINRNA splicing160/2587434/187233.74e-341.12e-30160
GO:000037520EsophagusHGINRNA splicing, via transesterification reactions115/2587324/187233.16e-233.80e-20115
GO:000037720EsophagusHGINRNA splicing, via transesterification reactions with bulged adenosine as nucleophile113/2587320/187231.24e-229.26e-20113
GO:000039820EsophagusHGINmRNA splicing, via spliceosome113/2587320/187231.24e-229.26e-20113
GO:000641727EsophagusHGINregulation of translation139/2587468/187231.46e-197.98e-17139
GO:000641320EsophagusHGINtranslational initiation55/2587118/187237.33e-182.31e-1555
GO:190331120EsophagusHGINregulation of mRNA metabolic process91/2587288/187235.06e-159.78e-1391
GO:005068419EsophagusHGINregulation of mRNA processing55/2587137/187232.17e-143.94e-1255
GO:000640320EsophagusHGINRNA localization66/2587201/187234.06e-125.41e-1066
GO:000644610EsophagusHGINregulation of translational initiation34/258779/187232.09e-101.97e-0834
GO:000691319EsophagusHGINnucleocytoplasmic transport83/2587301/187232.14e-101.97e-0883
GO:005116919EsophagusHGINnuclear transport83/2587301/187232.14e-101.97e-0883
GO:000640120EsophagusHGINRNA catabolic process77/2587278/187237.63e-106.36e-0877
GO:000640220EsophagusHGINmRNA catabolic process67/2587232/187231.47e-091.13e-0767
GO:000095617EsophagusHGINnuclear-transcribed mRNA catabolic process40/2587112/187234.44e-093.03e-0740
GO:003465519EsophagusHGINnucleobase-containing compound catabolic process98/2587407/187231.44e-088.94e-0798
GO:005116819EsophagusHGINnuclear export48/2587154/187232.21e-081.34e-0648
GO:004670017EsophagusHGINheterocycle catabolic process103/2587445/187235.44e-082.99e-06103
GO:005065716EsophagusHGINnucleic acid transport49/2587163/187235.71e-083.06e-0649
GO:005065816EsophagusHGINRNA transport49/2587163/187235.71e-083.06e-0649
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa0304018EsophagusHGINSpliceosome79/1383217/84653.22e-137.00e-125.56e-1279
hsa030159EsophagusHGINmRNA surveillance pathway30/138397/84652.48e-042.69e-032.14e-0330
hsa030137EsophagusHGINNucleocytoplasmic transport31/1383108/84658.29e-047.95e-036.31e-0331
hsa0304019EsophagusHGINSpliceosome79/1383217/84653.22e-137.00e-125.56e-1279
hsa0301514EsophagusHGINmRNA surveillance pathway30/138397/84652.48e-042.69e-032.14e-0330
hsa0301312EsophagusHGINNucleocytoplasmic transport31/1383108/84658.29e-047.95e-036.31e-0331
hsa0301321EsophagusESCCNucleocytoplasmic transport89/4205108/84651.20e-122.37e-111.21e-1189
hsa0301524EsophagusESCCmRNA surveillance pathway72/420597/84656.12e-074.10e-062.10e-0672
hsa0304027EsophagusESCCSpliceosome128/4205217/84653.31e-038.79e-034.50e-03128
hsa0301331EsophagusESCCNucleocytoplasmic transport89/4205108/84651.20e-122.37e-111.21e-1189
hsa0301534EsophagusESCCmRNA surveillance pathway72/420597/84656.12e-074.10e-062.10e-0672
hsa0304037EsophagusESCCSpliceosome128/4205217/84653.31e-038.79e-034.50e-03128
hsa030407LiverCirrhoticSpliceosome102/2530217/84655.69e-089.47e-075.84e-07102
hsa030154LiverCirrhoticmRNA surveillance pathway46/253097/84651.92e-041.30e-038.03e-0446
hsa0304012LiverCirrhoticSpliceosome102/2530217/84655.69e-089.47e-075.84e-07102
hsa0301511LiverCirrhoticmRNA surveillance pathway46/253097/84651.92e-041.30e-038.03e-0446
hsa03013LiverHCCNucleocytoplasmic transport81/4020108/84654.28e-096.83e-083.80e-0881
hsa0301521LiverHCCmRNA surveillance pathway66/402097/84653.16e-051.88e-041.04e-0466
hsa0304022LiverHCCSpliceosome122/4020217/84655.55e-031.60e-028.91e-03122
hsa030131LiverHCCNucleocytoplasmic transport81/4020108/84654.28e-096.83e-083.80e-0881
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Cell-cell communication analysis

check buttonIdentification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states
LigandReceptorLRpairPathwayTissueDisease Stage
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Single-cell gene regulatory network inference analysis

check buttonFind out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states
TFCell TypeTissueDisease StageTarget GeneRSSRegulon Activity
∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.
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Somatic mutation of malignant transformation related genes

check buttonAnnotation of somatic variants for genes involved in malignant transformation
Hugo SymbolVariant ClassVariant ClassificationdbSNP RSHGVScHGVSpHGVSp ShortSWISSPROTBIOTYPESIFTPolyPhenTumor Sample BarcodeTissueHistologySexAgeStageTherapy TypesDrugsOutcome
NCBP2SNVMissense_Mutationrs775717046c.440N>Cp.Gly147Alap.G147AP52298protein_codingdeleterious(0.01)probably_damaging(0.999)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
NCBP2insertionNonsense_Mutationnovelc.301_302insAGTGCATATGTCCTGCTTGAAATGTTCACATTGTGGCATCTGAACp.Ile101delinsLysCysIleCysProAlaTerAsnValHisIleValAlaSerGluLeup.I101delinsKCICPA*NVHIVASELP52298protein_codingTCGA-A8-A06X-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
NCBP2deletionFrame_Shift_Delnovelc.49delNp.Leu17Terp.L17*P52298protein_codingTCGA-EW-A2FV-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapydocetaxelSD
NCBP2SNVMissense_Mutationc.403N>Tp.Arg135Trpp.R135WP52298protein_codingdeleterious(0)probably_damaging(0.998)TCGA-EA-A410-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
NCBP2SNVMissense_Mutationnovelc.160N>Ap.Glu54Lysp.E54KP52298protein_codingdeleterious(0.02)benign(0.385)TCGA-AA-3972-01Colorectumcolon adenocarcinomaMale>=65III/IVChemotherapycapecitabinePD
NCBP2SNVMissense_Mutationc.295N>Tp.Arg99Trpp.R99WP52298protein_codingtolerated(0.17)benign(0.176)TCGA-AD-A5EJ-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownSD
NCBP2SNVMissense_Mutationc.455N>Cp.Leu152Prop.L152PP52298protein_codingtolerated(0.14)benign(0.005)TCGA-AZ-6598-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownSD
NCBP2SNVMissense_Mutationnovelc.340N>Tp.Asp114Tyrp.D114YP52298protein_codingdeleterious(0)probably_damaging(0.999)TCGA-F5-6814-01Colorectumrectum adenocarcinomaMale<65I/IIUnknownUnknownSD
NCBP2SNVMissense_Mutationc.334N>Tp.Arg112Cysp.R112CP52298protein_codingdeleterious(0.05)benign(0.35)TCGA-AJ-A3BH-01Endometriumuterine corpus endometrioid carcinomaFemaleUnknownI/IIUnknownUnknownSD
NCBP2SNVMissense_Mutationnovelc.103N>Ap.Leu35Ilep.L35IP52298protein_codingtolerated(0.2)benign(0.009)TCGA-AJ-A3EL-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
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Related drugs of malignant transformation related genes

check buttonIdentification of chemicals and drugs interact with genes involved in malignant transfromation
(DGIdb 4.0)
Entrez IDSymbolCategoryInteraction TypesDrug Claim NameDrug NamePMIDs
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