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: HHLA3

Gene summary for HHLA3

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

HHLA3

Gene ID

11147

Gene nameHERV-H LTR-associating 3
Gene AliasHHLA3
Cytomap1p31.1
Gene TypencRNA
GO ID

GO:0003674

UniProtAcc

NA


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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
11147HHLA3HCC1_MengHumanLiverHCC1.84e-517.91e-020.0246
11147HHLA3HCC2_MengHumanLiverHCC7.03e-034.91e-040.0107
11147HHLA3HCC1HumanLiverHCC8.50e-062.74e+000.5336
11147HHLA3S014HumanLiverHCC3.51e-124.07e-010.2254
11147HHLA3S015HumanLiverHCC4.03e-075.06e-010.2375
11147HHLA3S016HumanLiverHCC2.36e-103.75e-010.2243
11147HHLA3S028HumanLiverHCC2.29e-032.39e-010.2503
11147HHLA3S029HumanLiverHCC2.67e-053.57e-010.2581
11147HHLA3C04HumanOral cavityOSCC3.19e-179.01e-010.2633
11147HHLA3C21HumanOral cavityOSCC1.71e-134.47e-010.2678
11147HHLA3C30HumanOral cavityOSCC2.47e-104.40e-010.3055
11147HHLA3C43HumanOral cavityOSCC9.31e-071.61e-010.1704
11147HHLA3C46HumanOral cavityOSCC2.02e-082.91e-010.1673
11147HHLA3C57HumanOral cavityOSCC1.43e-063.15e-010.1679
11147HHLA3C06HumanOral cavityOSCC1.42e-035.95e-010.2699
11147HHLA3C08HumanOral cavityOSCC9.22e-081.73e-010.1919
11147HHLA3C09HumanOral cavityOSCC5.44e-042.34e-010.1431
11147HHLA3LN46HumanOral cavityOSCC3.69e-063.17e-010.1666
11147HHLA3LP17HumanOral cavityLP2.39e-055.83e-010.2349
11147HHLA3SYSMH2HumanOral cavityOSCC7.28e-031.39e-010.2326
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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
∗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
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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
HHLA3SNVMissense_Mutationnovelc.61G>Ap.Glu21Lysp.E21KQ9XRX5protein_codingdeleterious_low_confidence(0.02)benign(0.068)TCGA-BH-A42V-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
HHLA3SNVMissense_Mutationc.360N>Tp.Lys120Asnp.K120NQ9XRX5protein_codingpossibly_damaging(0.607)TCGA-CA-6718-01Colorectumcolon adenocarcinomaMale<65I/IIUnknownUnknownPD
HHLA3SNVMissense_Mutationnovelc.154G>Cp.Ala52Prop.A52PQ9XRX5protein_codingdeleterious_low_confidence(0.02)possibly_damaging(0.898)TCGA-AG-3726-01Colorectumrectum adenocarcinomaFemale<65I/IIUnknownUnknownSD
HHLA3SNVMissense_Mutationc.172G>Ap.Gly58Argp.G58RQ9XRX5protein_codingdeleterious_low_confidence(0.04)benign(0.007)TCGA-AG-4015-01Colorectumrectum adenocarcinomaFemale>=65I/IIUnknownUnknownSD
HHLA3SNVMissense_Mutationnovelc.146T>Gp.Leu49Argp.L49RQ9XRX5protein_codingdeleterious_low_confidence(0)benign(0.422)TCGA-AG-A002-01Colorectumrectum adenocarcinomaMale<65I/IIUnknownUnknownSD
HHLA3SNVMissense_Mutationc.163N>Ap.Leu55Ilep.L55IQ9XRX5protein_codingdeleterious_low_confidence(0)possibly_damaging(0.567)TCGA-BS-A0UF-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
HHLA3SNVMissense_Mutationc.325N>Ap.Ser109Thrp.S109TQ9XRX5protein_codingbenign(0.294)TCGA-BS-A0UJ-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
HHLA3SNVMissense_Mutationnovelc.130A>Gp.Thr44Alap.T44AQ9XRX5protein_codingtolerated_low_confidence(0.1)benign(0.062)TCGA-F7-A624-01Oral cavityhead & neck squamous cell carcinomaMale>=65I/IIUnknownUnknownSD
HHLA3SNVMissense_Mutationnovelc.55N>Ap.Ala19Thrp.A19TQ9XRX5protein_codingdeleterious_low_confidence(0.01)possibly_damaging(0.665)TCGA-UF-A7JO-01Oral cavityhead & neck squamous cell carcinomaFemale>=65I/IIUnknownUnknownPD
HHLA3SNVMissense_Mutationc.49C>Tp.Pro17Serp.P17SQ9XRX5protein_codingdeleterious_low_confidence(0.04)benign(0.22)TCGA-D7-A4YV-01Stomachstomach adenocarcinomaFemale>=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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