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: COA4

Gene summary for COA4

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

COA4

Gene ID

51287

Gene namecytochrome c oxidase assembly factor 4 homolog
Gene AliasCHCHD8
Cytomap11q13.4
Gene Typeprotein-coding
GO ID

GO:0006996

UniProtAcc

A0A024R5J6


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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
51287COA4GSM4909281HumanBreastIDC2.20e-032.85e-010.21
51287COA4GSM4909282HumanBreastIDC1.63e-053.70e-01-0.0288
51287COA4GSM4909286HumanBreastIDC9.16e-052.86e-010.1081
51287COA4GSM4909290HumanBreastIDC1.70e-186.19e-010.2096
51287COA4GSM4909296HumanBreastIDC7.33e-056.73e-020.1524
51287COA4GSM4909297HumanBreastIDC2.89e-07-1.28e-010.1517
51287COA4GSM4909307HumanBreastIDC9.59e-063.50e-010.1569
51287COA4GSM4909308HumanBreastIDC1.71e-083.58e-010.158
51287COA4GSM4909311HumanBreastIDC3.08e-15-1.59e-010.1534
51287COA4GSM4909312HumanBreastIDC5.60e-035.84e-020.1552
51287COA4GSM4909319HumanBreastIDC1.21e-23-6.02e-020.1563
51287COA4GSM4909320HumanBreastIDC1.69e-073.70e-010.1575
51287COA4GSM4909321HumanBreastIDC6.44e-101.44e-010.1559
51287COA4brca1HumanBreastPrecancer6.06e-043.16e-01-0.0338
51287COA4brca2HumanBreastPrecancer8.63e-032.11e-01-0.024
51287COA4M2HumanBreastIDC2.47e-023.14e-010.21
51287COA4NCCBC14HumanBreastDCIS1.13e-052.39e-010.2021
51287COA4NCCBC2HumanBreastDCIS3.11e-041.65e-010.1554
51287COA4P1HumanBreastIDC5.79e-07-1.36e-020.1527
51287COA4P3HumanBreastIDC4.95e-045.77e-010.1542
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
BreastThe 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.IDC: Invasive ductal carcinoma
DCIS: Ductal carcinoma in situ
Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
Colorectum (GSE201348)The 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.FAP: Familial adenomatous polyposis
CRC: Colorectal cancer
Colorectum (HTA11)The 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.AD: Adenomas
SER: Sessile serrated lesions
MSI-H: Microsatellite-high colorectal cancer
MSS: Microsatellite stable colorectal cancer
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
ProstateThe 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.BPH: Benign Prostatic Hyperplasia
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:0030520ColorectumMSSintracellular estrogen receptor signaling pathway21/346754/187233.68e-044.66e-0321
GO:00550722ColorectumMSSiron ion homeostasis29/346785/187234.44e-045.32e-0329
GO:00070411ColorectumMSSlysosomal transport36/3467114/187235.38e-046.04e-0336
GO:00469162ColorectumMSScellular transition metal ion homeostasis35/3467115/187231.33e-031.26e-0235
GO:00726652ColorectumMSSprotein localization to vacuole23/346767/187231.51e-031.39e-0223
GO:00068791ColorectumMSScellular iron ion homeostasis22/346767/187233.57e-032.64e-0222
GO:00713833ColorectumFAPcellular response to steroid hormone stimulus59/2622204/187232.12e-082.06e-0659
GO:00485454ColorectumFAPresponse to steroid hormone81/2622339/187236.22e-073.08e-0581
GO:00725944ColorectumFAPestablishment of protein localization to organelle96/2622422/187236.63e-073.20e-0596
GO:00305223ColorectumFAPintracellular receptor signaling pathway67/2622265/187236.84e-073.28e-0567
GO:00434014ColorectumFAPsteroid hormone mediated signaling pathway41/2622136/187238.82e-074.03e-0541
GO:00097554ColorectumFAPhormone-mediated signaling pathway51/2622190/187232.23e-068.87e-0551
GO:00066054ColorectumFAPprotein targeting74/2622314/187233.21e-061.17e-0474
GO:00305183ColorectumFAPintracellular steroid hormone receptor signaling pathway34/2622116/187231.43e-053.80e-0434
GO:00070343ColorectumFAPvacuolar transport40/2622157/187239.41e-051.61e-0340
GO:19016544ColorectumFAPresponse to ketone45/2622194/187233.67e-044.63e-0345
GO:00070412ColorectumFAPlysosomal transport30/2622114/187233.71e-044.63e-0330
GO:00614583ColorectumFAPreproductive system development85/2622427/187234.30e-045.13e-0385
GO:00486083ColorectumFAPreproductive structure development84/2622424/187235.40e-046.10e-0384
GO:00066231ColorectumFAPprotein targeting to vacuole13/262237/187231.03e-031.00e-0213
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa0471418BreastPrecancerThermogenesis68/684232/84654.40e-221.26e-209.69e-2168
hsa0471419BreastPrecancerThermogenesis68/684232/84654.40e-221.26e-209.69e-2168
hsa0471424BreastIDCThermogenesis75/867232/84658.41e-213.04e-192.27e-1975
hsa0471434BreastIDCThermogenesis75/867232/84658.41e-213.04e-192.27e-1975
hsa0471443BreastDCISThermogenesis74/846232/84658.72e-213.13e-192.30e-1974
hsa0471453BreastDCISThermogenesis74/846232/84658.72e-213.13e-192.30e-1974
hsa04714ColorectumADThermogenesis120/2092232/84652.76e-191.16e-177.37e-18120
hsa047141ColorectumADThermogenesis120/2092232/84652.76e-191.16e-177.37e-18120
hsa047142ColorectumSERThermogenesis106/1580232/84651.15e-216.34e-204.61e-20106
hsa047143ColorectumSERThermogenesis106/1580232/84651.15e-216.34e-204.61e-20106
hsa047144ColorectumMSSThermogenesis113/1875232/84651.52e-194.62e-182.83e-18113
hsa047145ColorectumMSSThermogenesis113/1875232/84651.52e-194.62e-182.83e-18113
hsa0471439EsophagusHGINThermogenesis91/1383232/84651.97e-175.36e-164.25e-1691
hsa04714114EsophagusHGINThermogenesis91/1383232/84651.97e-175.36e-164.25e-1691
hsa04714211EsophagusESCCThermogenesis163/4205232/84659.22e-111.14e-095.86e-10163
hsa04714310EsophagusESCCThermogenesis163/4205232/84659.22e-111.14e-095.86e-10163
hsa0471414LiverCirrhoticThermogenesis121/2530232/84655.70e-131.36e-118.36e-12121
hsa0471415LiverCirrhoticThermogenesis121/2530232/84655.70e-131.36e-118.36e-12121
hsa0471422LiverHCCThermogenesis170/4020232/84655.36e-162.25e-141.25e-14170
hsa0471432LiverHCCThermogenesis170/4020232/84655.36e-162.25e-141.25e-14170
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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
COA4SNVMissense_Mutationc.223N>Ap.Glu75Lysp.E75KQ9NYJ1protein_codingdeleterious(0.01)benign(0.111)TCGA-AR-A0TX-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
COA4SNVMissense_Mutationc.148N>Ap.Asp50Asnp.D50NQ9NYJ1protein_codingdeleterious(0)probably_damaging(0.994)TCGA-EK-A2R8-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
COA4SNVMissense_Mutationrs146693705c.92G>Ap.Arg31Hisp.R31HQ9NYJ1protein_codingtolerated(0.15)benign(0.012)TCGA-AZ-4315-01Colorectumcolon adenocarcinomaMale<65I/IIUnknownUnknownSD
COA4SNVMissense_Mutationrs143220644c.209N>Tp.Ala70Valp.A70VQ9NYJ1protein_codingtolerated(0.27)benign(0.003)TCGA-A5-A0G2-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVUnknownUnknownSD
COA4SNVMissense_Mutationnovelc.185N>Tp.Lys62Metp.K62MQ9NYJ1protein_codingdeleterious(0)possibly_damaging(0.807)TCGA-EC-A1NJ-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
COA4insertionFrame_Shift_Insnovelc.105_106insAATTTTTGTATTTTTAGTAGAGAATGp.Ala36AsnfsTer39p.A36Nfs*39Q9NYJ1protein_codingTCGA-A5-A0G5-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
COA4SNVMissense_Mutationnovelc.212G>Tp.Arg71Metp.R71MQ9NYJ1protein_codingdeleterious(0.01)benign(0.254)TCGA-73-A9RS-01Lunglung adenocarcinomaMale<65I/IIChemotherapycarboplatinPD
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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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