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: ATP5MF

Gene summary for ATP5MF

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

ATP5MF

Gene ID

9551

Gene nameATP synthase membrane subunit f
Gene AliasATP5J2
Cytomap7q22.1
Gene Typeprotein-coding
GO ID

GO:0006091

UniProtAcc

P56134


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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
9551ATP5MFGSM4909281HumanBreastIDC4.10e-155.11e-010.21
9551ATP5MFGSM4909282HumanBreastIDC7.49e-276.73e-01-0.0288
9551ATP5MFGSM4909285HumanBreastIDC2.00e-142.25e-010.21
9551ATP5MFGSM4909286HumanBreastIDC1.23e-275.26e-010.1081
9551ATP5MFGSM4909287HumanBreastIDC1.16e-033.59e-010.2057
9551ATP5MFGSM4909288HumanBreastIDC1.32e-034.41e-010.0988
9551ATP5MFGSM4909289HumanBreastIDC3.92e-025.10e-010.1064
9551ATP5MFGSM4909290HumanBreastIDC9.57e-094.53e-010.2096
9551ATP5MFGSM4909291HumanBreastIDC6.61e-054.29e-010.1753
9551ATP5MFGSM4909293HumanBreastIDC1.02e-236.02e-010.1581
9551ATP5MFGSM4909294HumanBreastIDC3.21e-104.77e-010.2022
9551ATP5MFGSM4909295HumanBreastIDC1.01e-024.02e-010.0898
9551ATP5MFGSM4909296HumanBreastIDC2.53e-438.21e-010.1524
9551ATP5MFGSM4909297HumanBreastIDC1.35e-045.19e-020.1517
9551ATP5MFGSM4909298HumanBreastIDC1.01e-103.92e-010.1551
9551ATP5MFGSM4909299HumanBreastIDC5.24e-043.23e-010.035
9551ATP5MFGSM4909301HumanBreastIDC2.92e-297.35e-010.1577
9551ATP5MFGSM4909302HumanBreastIDC1.07e-023.00e-010.1545
9551ATP5MFGSM4909304HumanBreastIDC1.74e-408.06e-010.1636
9551ATP5MFGSM4909306HumanBreastIDC9.54e-104.81e-010.1564
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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
CervixThe 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.CC: Cervix cancer
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
N_HPV: HPV-infected normal cervix
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
EndometriumThe 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.AEH: Atypical endometrial hyperplasia
EEC: Endometrioid 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
GCThe 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.CAG: Chronic atrophic gastritis
CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
CSG: Chronic superficial gastritis
GC: Gastric cancer
SIM: Severe intestinal metaplasia
WIM: Wild intestinal metaplasia
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
LungThe 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.AAH: Atypical adenomatous hyperplasia
AIS: Adenocarcinoma in situ
IAC: Invasive lung adenocarcinoma
MIA: Minimally invasive adenocarcinoma
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:004533333ThyroidATCcellular respiration140/6293230/187231.76e-171.89e-15140
GO:000683929ThyroidATCmitochondrial transport151/6293254/187232.07e-172.14e-15151
GO:000611933ThyroidATCoxidative phosphorylation96/6293141/187235.40e-174.88e-1596
GO:001598034ThyroidATCenergy derivation by oxidation of organic compounds177/6293318/187233.60e-162.92e-14177
GO:001969328ThyroidATCribose phosphate metabolic process184/6293396/187235.87e-081.05e-06184
GO:000915029ThyroidATCpurine ribonucleotide metabolic process172/6293368/187239.58e-081.64e-06172
GO:000925928ThyroidATCribonucleotide metabolic process178/6293385/187231.47e-072.39e-06178
GO:000914427ThyroidATCpurine nucleoside triphosphate metabolic process53/629388/187232.75e-074.20e-0653
GO:007252128ThyroidATCpurine-containing compound metabolic process189/6293416/187232.83e-074.29e-06189
GO:0006753111ThyroidATCnucleoside phosphate metabolic process219/6293497/187235.92e-078.29e-06219
GO:000914128ThyroidATCnucleoside triphosphate metabolic process63/6293112/187236.90e-079.35e-0663
GO:0009117112ThyroidATCnucleotide metabolic process215/6293489/187239.09e-071.20e-05215
GO:000920527ThyroidATCpurine ribonucleoside triphosphate metabolic process49/629382/187231.07e-061.39e-0549
GO:000616328ThyroidATCpurine nucleotide metabolic process177/6293396/187232.39e-062.82e-05177
GO:199054226ThyroidATCmitochondrial transmembrane transport57/6293102/187233.05e-063.49e-0557
GO:000919926ThyroidATCribonucleoside triphosphate metabolic process51/629389/187233.72e-064.12e-0551
GO:000914527ThyroidATCpurine nucleoside triphosphate biosynthetic process41/629369/187239.68e-069.67e-0541
GO:000915225ThyroidATCpurine ribonucleotide biosynthetic process84/6293169/187231.05e-051.04e-0484
GO:004639025ThyroidATCribose phosphate biosynthetic process92/6293190/187231.57e-051.46e-0492
GO:000920627ThyroidATCpurine ribonucleoside triphosphate biosynthetic process40/629368/187231.74e-051.59e-0440
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa0019016BreastPrecancerOxidative phosphorylation59/684134/84656.15e-303.24e-282.48e-2859
hsa0471418BreastPrecancerThermogenesis68/684232/84654.40e-221.26e-209.69e-2168
hsa0019017BreastPrecancerOxidative phosphorylation59/684134/84656.15e-303.24e-282.48e-2859
hsa0471419BreastPrecancerThermogenesis68/684232/84654.40e-221.26e-209.69e-2168
hsa0019023BreastIDCOxidative phosphorylation62/867134/84654.78e-272.59e-251.94e-2562
hsa0471424BreastIDCThermogenesis75/867232/84658.41e-213.04e-192.27e-1975
hsa0019033BreastIDCOxidative phosphorylation62/867134/84654.78e-272.59e-251.94e-2562
hsa0471434BreastIDCThermogenesis75/867232/84658.41e-213.04e-192.27e-1975
hsa0019043BreastDCISOxidative phosphorylation61/846134/84659.84e-275.30e-253.90e-2561
hsa0471443BreastDCISThermogenesis74/846232/84658.72e-213.13e-192.30e-1974
hsa0019053BreastDCISOxidative phosphorylation61/846134/84659.84e-275.30e-253.90e-2561
hsa0471453BreastDCISThermogenesis74/846232/84658.72e-213.13e-192.30e-1974
hsa0019018CervixCCOxidative phosphorylation64/1267134/84651.25e-198.07e-184.77e-1864
hsa0471420CervixCCThermogenesis76/1267232/84654.29e-121.16e-106.85e-1176
hsa0019019CervixCCOxidative phosphorylation64/1267134/84651.25e-198.07e-184.77e-1864
hsa04714110CervixCCThermogenesis76/1267232/84654.29e-121.16e-106.85e-1176
hsa00190ColorectumADOxidative phosphorylation86/2092134/84652.47e-222.76e-201.76e-2086
hsa04714ColorectumADThermogenesis120/2092232/84652.76e-191.16e-177.37e-18120
hsa001901ColorectumADOxidative phosphorylation86/2092134/84652.47e-222.76e-201.76e-2086
hsa047141ColorectumADThermogenesis120/2092232/84652.76e-191.16e-177.37e-18120
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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
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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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