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:00331088BreastPrecancermitochondrial respiratory chain complex assembly24/108093/187233.39e-103.16e-0824
GO:003310813BreastIDCmitochondrial respiratory chain complex assembly28/143493/187231.54e-101.83e-0828
GO:003310823BreastDCISmitochondrial respiratory chain complex assembly28/139093/187237.50e-119.43e-0928
GO:0072594ColorectumADestablishment of protein localization to organelle148/3918422/187237.95e-121.04e-09148
GO:0033108ColorectumADmitochondrial respiratory chain complex assembly46/391893/187238.95e-106.91e-0846
GO:0006605ColorectumADprotein targeting105/3918314/187231.39e-076.44e-06105
GO:0007034ColorectumADvacuolar transport60/3918157/187234.97e-071.85e-0560
GO:0071383ColorectumADcellular response to steroid hormone stimulus73/3918204/187236.31e-072.24e-0573
GO:0055076ColorectumADtransition metal ion homeostasis53/3918138/187231.89e-065.65e-0553
GO:0030522ColorectumADintracellular receptor signaling pathway87/3918265/187233.69e-061.03e-0487
GO:0043401ColorectumADsteroid hormone mediated signaling pathway51/3918136/187236.52e-061.63e-0451
GO:0048545ColorectumADresponse to steroid hormone104/3918339/187231.33e-052.90e-04104
GO:0009755ColorectumADhormone-mediated signaling pathway64/3918190/187232.78e-055.24e-0464
GO:0046916ColorectumADcellular transition metal ion homeostasis43/3918115/187233.62e-056.56e-0443
GO:0030518ColorectumADintracellular steroid hormone receptor signaling pathway43/3918116/187234.61e-057.97e-0443
GO:0007041ColorectumADlysosomal transport42/3918114/187236.61e-051.07e-0342
GO:0072665ColorectumADprotein localization to vacuole27/391867/187232.40e-043.04e-0327
GO:0055072ColorectumADiron ion homeostasis32/391885/187232.97e-043.60e-0332
GO:0061458ColorectumADreproductive system development116/3918427/187231.11e-031.01e-02116
GO:1901654ColorectumADresponse to ketone59/3918194/187231.14e-031.04e-0259
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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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