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: TET1

Gene summary for TET1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

TET1

Gene ID

80312

Gene nametet methylcytosine dioxygenase 1
Gene AliasCXXC6
Cytomap10q21.3
Gene Typeprotein-coding
GO ID

GO:0001701

UniProtAcc

Q8NFU7


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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
80312TET1PTC05HumanThyroidPTC1.26e-113.96e-010.2065
80312TET1PTC07HumanThyroidPTC1.21e-041.02e-010.2044
80312TET1ATC12HumanThyroidATC4.25e-142.86e-010.34
80312TET1ATC13HumanThyroidATC7.21e-446.86e-010.34
80312TET1ATC4HumanThyroidATC7.37e-163.82e-010.34
80312TET1ATC5HumanThyroidATC2.11e-467.42e-010.34
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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:001657010ThyroidPTChistone modification235/5968463/187231.17e-171.15e-15235
GO:0046700111ThyroidPTCheterocycle catabolic process221/5968445/187232.43e-151.72e-13221
GO:0044270111ThyroidPTCcellular nitrogen compound catabolic process223/5968451/187233.34e-152.31e-13223
GO:0019439111ThyroidPTCaromatic compound catabolic process225/5968467/187238.51e-144.71e-12225
GO:1901361111ThyroidPTCorganic cyclic compound catabolic process231/5968495/187232.55e-121.12e-10231
GO:0001701111ThyroidPTCin utero embryonic development175/5968367/187231.40e-104.73e-09175
GO:003105610ThyroidPTCregulation of histone modification83/5968152/187235.19e-091.34e-0783
GO:000632520ThyroidPTCchromatin organization183/5968409/187232.55e-085.70e-07183
GO:00310585ThyroidPTCpositive regulation of histone modification53/596892/187233.03e-075.13e-0653
GO:00400297ThyroidPTCregulation of gene expression, epigenetic57/5968105/187231.60e-062.25e-0557
GO:00310626ThyroidPTCpositive regulation of histone methylation26/596841/187233.23e-053.07e-0426
GO:001657110ThyroidPTChistone methylation67/5968141/187237.31e-056.31e-0467
GO:000647910ThyroidPTCprotein methylation82/5968181/187231.01e-048.21e-0482
GO:000821310ThyroidPTCprotein alkylation82/5968181/187231.01e-048.21e-0482
GO:00310606ThyroidPTCregulation of histone methylation37/596869/187231.46e-041.13e-0337
GO:009872710ThyroidPTCmaintenance of cell number63/5968134/187231.73e-041.32e-0363
GO:00198279ThyroidPTCstem cell population maintenance61/5968131/187233.01e-042.12e-0361
GO:00322594ThyroidPTCmethylation146/5968364/187234.99e-043.26e-03146
GO:000182513ThyroidPTCblastocyst formation22/596838/187238.19e-045.07e-0322
GO:00434145ThyroidPTCmacromolecule methylation127/5968316/187231.02e-036.07e-03127
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
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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
TET1ECMLungAAHGPR137C,AP001636.3,PLEKHA7, etc.4.29e-01The 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.
TET1ECMLungADJGPR137C,AP001636.3,PLEKHA7, etc.3.95e-01The 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.
TET1MYOFIBLungADJGPR137C,AP001636.3,PLEKHA7, etc.1.81e-01The 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.
TET1FIBLungADJGPR137C,AP001636.3,PLEKHA7, etc.1.29e-02The 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.
TET1ECMLungAISGPR137C,AP001636.3,PLEKHA7, etc.4.29e-01The 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.
TET1FIBLungIACGPR137C,AP001636.3,PLEKHA7, etc.2.65e-02The 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.
TET1MYOFIBLungIACGPR137C,AP001636.3,PLEKHA7, etc.3.10e-01The 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.
TET1ECMLungMIACGPR137C,AP001636.3,PLEKHA7, etc.3.90e-01The 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.
∗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
TET1SNVMissense_Mutationnovelc.3184N>Ap.Asp1062Asnp.D1062NQ8NFU7protein_codingtolerated(0.2)benign(0.006)TCGA-3C-AALI-01Breastbreast invasive carcinomaFemale<65I/IIUnspecificPoly EComplete Response
TET1SNVMissense_Mutationrs778536892c.23G>Ap.Arg8Lysp.R8KQ8NFU7protein_codingtolerated(0.49)benign(0.018)TCGA-A2-A0T0-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapytaxotereSD
TET1SNVMissense_Mutationnovelc.4185T>Ap.Phe1395Leup.F1395LQ8NFU7protein_codingtolerated(0.06)probably_damaging(0.997)TCGA-A7-A0CG-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
TET1SNVMissense_Mutationc.1580C>Tp.Ser527Leup.S527LQ8NFU7protein_codingtolerated(0.12)benign(0)TCGA-A8-A0A7-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
TET1SNVMissense_Mutationnovelc.3095N>Tp.Ser1032Phep.S1032FQ8NFU7protein_codingtolerated(0.09)benign(0.021)TCGA-AC-A3BB-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapycytoxanCR
TET1SNVMissense_Mutationnovelc.554N>Ap.Ser185Asnp.S185NQ8NFU7protein_codingtolerated(0.15)possibly_damaging(0.459)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
TET1SNVMissense_Mutationnovelc.984N>Cp.Lys328Asnp.K328NQ8NFU7protein_codingdeleterious(0.04)benign(0.007)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
TET1SNVMissense_Mutationrs538486517c.1452N>Tp.Glu484Aspp.E484DQ8NFU7protein_codingdeleterious(0.02)benign(0.28)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
TET1SNVMissense_Mutationrs369109149c.2234N>Ap.Arg745Glnp.R745QQ8NFU7protein_codingtolerated(0.59)benign(0)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
TET1SNVMissense_Mutationnovelc.2594N>Cp.Lys865Thrp.K865TQ8NFU7protein_codingtolerated(0.12)benign(0.01)TCGA-AN-A046-01Breastbreast invasive 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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