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: CLIP3

Gene summary for CLIP3

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

CLIP3

Gene ID

25999

Gene nameCAP-Gly domain containing linker protein 3
Gene AliasCLIPR-59
Cytomap19q13.12
Gene Typeprotein-coding
GO ID

GO:0000226

UniProtAcc

Q96DZ5


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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
25999CLIP3male-WTAHumanThyroidPTC2.76e-081.42e-010.1037
25999CLIP3PTC05HumanThyroidPTC2.31e-021.51e-010.2065
25999CLIP3PTC07HumanThyroidPTC1.09e-027.59e-020.2044
25999CLIP3ATC13HumanThyroidATC1.75e-559.86e-010.34
25999CLIP3ATC5HumanThyroidATC5.88e-571.04e+000.34
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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:1903829113ThyroidPTCpositive regulation of cellular protein localization162/5968276/187232.40e-203.52e-18162
GO:1902903113ThyroidPTCregulation of supramolecular fiber organization202/5968383/187231.16e-171.15e-15202
GO:0043254113ThyroidPTCregulation of protein-containing complex assembly215/5968428/187231.23e-159.09e-14215
GO:0072659112ThyroidPTCprotein localization to plasma membrane153/5968284/187239.90e-156.50e-13153
GO:1990778111ThyroidPTCprotein localization to cell periphery172/5968333/187233.71e-142.30e-12172
GO:00435437ThyroidPTCprotein acylation134/5968243/187234.22e-142.58e-12134
GO:0051258113ThyroidPTCprotein polymerization154/5968297/187235.35e-132.66e-11154
GO:0032271113ThyroidPTCregulation of protein polymerization123/5968233/187232.45e-119.38e-10123
GO:0030705111ThyroidPTCcytoskeleton-dependent intracellular transport104/5968195/187233.87e-101.24e-08104
GO:0010639112ThyroidPTCnegative regulation of organelle organization163/5968348/187233.04e-098.39e-08163
GO:003010020ThyroidPTCregulation of endocytosis108/5968211/187233.92e-091.04e-07108
GO:007050717ThyroidPTCregulation of microtubule cytoskeleton organization80/5968148/187231.79e-084.19e-0780
GO:1904375111ThyroidPTCregulation of protein localization to cell periphery70/5968125/187232.04e-084.71e-0770
GO:190547525ThyroidPTCregulation of protein localization to membrane91/5968175/187232.41e-085.43e-0791
GO:004580720ThyroidPTCpositive regulation of endocytosis58/5968100/187236.11e-081.28e-0658
GO:00109709ThyroidPTCtransport along microtubule80/5968155/187232.48e-074.32e-0680
GO:1903076112ThyroidPTCregulation of protein localization to plasma membrane58/5968104/187233.91e-076.51e-0658
GO:004409110ThyroidPTCmembrane biogenesis34/596855/187234.64e-065.69e-0534
GO:00311229ThyroidPTCcytoplasmic microtubule organization34/596856/187238.20e-069.42e-0534
GO:190547725ThyroidPTCpositive regulation of protein localization to membrane55/5968106/187231.45e-051.55e-0455
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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
∗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
CLIP3SNVMissense_Mutationnovelc.748N>Ap.Glu250Lysp.E250KQ96DZ5protein_codingdeleterious(0.01)benign(0.321)TCGA-PE-A5DE-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapytaxotereCR
CLIP3SNVMissense_Mutationc.1213C>Gp.Leu405Valp.L405VQ96DZ5protein_codingtolerated(0.9)benign(0)TCGA-C5-A7UH-01Cervixcervical & endocervical cancerFemale<65III/IVChemotherapycisplatinSD
CLIP3SNVMissense_Mutationrs779187288c.461C>Tp.Thr154Metp.T154MQ96DZ5protein_codingdeleterious(0.02)possibly_damaging(0.761)TCGA-EA-A3HS-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
CLIP3SNVMissense_Mutationrs750880445c.197C>Tp.Ala66Valp.A66VQ96DZ5protein_codingtolerated(0.08)possibly_damaging(0.834)TCGA-EA-A3HU-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
CLIP3SNVMissense_Mutationc.343N>Ap.Gly115Argp.G115RQ96DZ5protein_codingdeleterious(0.04)probably_damaging(0.92)TCGA-EX-A1H5-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
CLIP3SNVMissense_Mutationrs370765485c.1298N>Ap.Arg433Hisp.R433HQ96DZ5protein_codingdeleterious(0.02)benign(0.005)TCGA-FU-A3HZ-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
CLIP3SNVMissense_Mutationnovelc.143C>Tp.Pro48Leup.P48LQ96DZ5protein_codingtolerated(0.06)benign(0.109)TCGA-ZJ-AAXB-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
CLIP3SNVMissense_Mutationnovelc.34N>Ap.Pro12Thrp.P12TQ96DZ5protein_codingdeleterious_low_confidence(0)benign(0.031)TCGA-ZJ-AB0I-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
CLIP3SNVMissense_Mutationrs772399672c.443C>Tp.Ala148Valp.A148VQ96DZ5protein_codingtolerated(0.26)benign(0.193)TCGA-5M-AAT6-01Colorectumcolon adenocarcinomaFemale<65III/IVUnknownUnknownPD
CLIP3SNVMissense_Mutationrs757632653c.1550G>Ap.Arg517Glnp.R517QQ96DZ5protein_codingtolerated(0.09)probably_damaging(0.953)TCGA-A6-2675-01Colorectumcolon adenocarcinomaMale>=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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