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: SLC6A4

Gene summary for SLC6A4

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

SLC6A4

Gene ID

6532

Gene namesolute carrier family 6 member 4
Gene Alias5-HTT
Cytomap17q11.2
Gene Typeprotein-coding
GO ID

GO:0000003

UniProtAcc

B2R7Y7


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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
6532SLC6A4HCC1HumanLiverHCC6.31e-221.30e+000.5336
6532SLC6A4HCC2HumanLiverHCC2.51e-231.37e+000.5341
6532SLC6A4HCC5HumanLiverHCC2.22e-281.26e+000.4932
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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
∗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:003166722LiverHCCresponse to nutrient levels276/7958474/187232.30e-121.08e-10276
GO:000758421LiverHCCresponse to nutrient111/7958174/187231.10e-082.73e-07111
GO:000963622LiverHCCresponse to toxic substance153/7958262/187231.37e-072.58e-06153
GO:000941022LiverHCCresponse to xenobiotic stimulus248/7958462/187236.47e-071.02e-05248
GO:000166612LiverHCCresponse to hypoxia172/7958307/187231.06e-061.59e-05172
GO:003629312LiverHCCresponse to decreased oxygen levels179/7958322/187231.29e-061.87e-05179
GO:007048212LiverHCCresponse to oxygen levels191/7958347/187231.42e-062.03e-05191
GO:004578711LiverHCCpositive regulation of cell cycle172/7958313/187235.29e-066.58e-05172
GO:000762321LiverHCCcircadian rhythm117/7958210/187237.29e-056.54e-04117
GO:00323552LiverHCCresponse to estradiol81/7958141/187232.39e-041.79e-0381
GO:001407421LiverHCCresponse to purine-containing compound84/7958148/187233.19e-042.26e-0384
GO:004851121LiverHCCrhythmic process156/7958298/187233.54e-042.46e-03156
GO:004668321LiverHCCresponse to organophosphorus73/7958131/187231.52e-038.05e-0373
GO:00459263LiverHCCnegative regulation of growth129/7958249/187231.81e-039.37e-03129
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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
SLC6A4SNVMissense_Mutationc.352C>Tp.Leu118Phep.L118FP31645protein_codingdeleterious(0)probably_damaging(1)TCGA-A2-A0SV-01Breastbreast invasive carcinomaFemale<65III/IVOther, specify in notesBisphosphonate therapyzometaPD
SLC6A4SNVMissense_Mutationrs774795329c.1316N>Tp.Thr439Metp.T439MP31645protein_codingdeleterious(0)probably_damaging(0.999)TCGA-A8-A09I-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyanastrozoleSD
SLC6A4SNVMissense_Mutationrs774252706c.38N>Tp.Ser13Leup.S13LP31645protein_codingtolerated_low_confidence(0.2)benign(0.003)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
SLC6A4SNVMissense_Mutationc.386N>Ap.Gly129Glup.G129EP31645protein_codingdeleterious(0)probably_damaging(1)TCGA-D8-A1J8-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapynolvadexSD
SLC6A4SNVMissense_Mutationc.221T>Gp.Leu74Argp.L74RP31645protein_codingtolerated(0.54)benign(0.003)TCGA-D8-A1XK-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicine+cyclophosphamideSD
SLC6A4SNVMissense_Mutationc.1159N>Ap.Ala387Thrp.A387TP31645protein_codingdeleterious(0)probably_damaging(0.938)TCGA-D8-A1XQ-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
SLC6A4SNVMissense_Mutationnovelc.540G>Ap.Met180Ilep.M180IP31645protein_codingtolerated(1)benign(0)TCGA-E2-A1LE-01Breastbreast invasive carcinomaFemale>=65III/IVChemotherapyherceptinPD
SLC6A4insertionNonsense_Mutationnovelc.1569_1570insTGACAAAGTGAGACTp.Arg523_Asp524insTerp.R523_D524ins*P31645protein_codingTCGA-AO-A0JB-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapycyclophosphamideSD
SLC6A4insertionNonsense_Mutationnovelc.1856_1857insTATCAGATACCAATGATCATACCAACAGAp.Glu619AspfsTer6p.E619Dfs*6P31645protein_codingTCGA-AR-A0U0-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
SLC6A4SNVMissense_Mutationc.1124N>Tp.Ser375Leup.S375LP31645protein_codingdeleterious(0.02)probably_damaging(0.99)TCGA-C5-A2LT-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinSD
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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
6532SLC6A4TRANSPORTER, DRUGGABLE GENOMEDULOXETINEDULOXETINE
6532SLC6A4TRANSPORTER, DRUGGABLE GENOMEbuprenorphineBUPRENORPHINE29333880
6532SLC6A4TRANSPORTER, DRUGGABLE GENOMEinhibitor178104007LEVOMILNACIPRAN
6532SLC6A4TRANSPORTER, DRUGGABLE GENOMEberberineBERBERINE21647174
6532SLC6A4TRANSPORTER, DRUGGABLE GENOMEinhibitor178103894VENLAFAXINE
6532SLC6A4TRANSPORTER, DRUGGABLE GENOMEDESVENLAFAXINEDESVENLAFAXINE
6532SLC6A4TRANSPORTER, DRUGGABLE GENOMEethanolALCOHOL31595439
6532SLC6A4TRANSPORTER, DRUGGABLE GENOMEVENLAFAXINEVENLAFAXINE
6532SLC6A4TRANSPORTER, DRUGGABLE GENOMEAMOXAPINEAMOXAPINE
6532SLC6A4TRANSPORTER, DRUGGABLE GENOMEAMOXAPINEAMOXAPINE
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