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: SPTLC2

Gene summary for SPTLC2

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

SPTLC2

Gene ID

9517

Gene nameserine palmitoyltransferase long chain base subunit 2
Gene AliasHSN1C
Cytomap14q24.3
Gene Typeprotein-coding
GO ID

GO:0006066

UniProtAcc

A0A024R6H1


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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
9517SPTLC2HTA11_3410_2000001011HumanColorectumAD7.47e-05-3.05e-010.0155
9517SPTLC2HTA11_347_2000001011HumanColorectumAD4.46e-136.73e-01-0.1954
9517SPTLC2HTA11_99999974143_84620HumanColorectumMSS2.90e-03-3.01e-010.3005
9517SPTLC2A001-C-207HumanColorectumFAP1.24e-02-2.14e-010.1278
9517SPTLC2A015-C-203HumanColorectumFAP8.90e-17-3.18e-01-0.1294
9517SPTLC2A015-C-204HumanColorectumFAP8.67e-07-2.98e-01-0.0228
9517SPTLC2A014-C-040HumanColorectumFAP4.38e-06-5.61e-01-0.1184
9517SPTLC2A002-C-201HumanColorectumFAP2.29e-11-3.41e-010.0324
9517SPTLC2A001-C-119HumanColorectumFAP5.43e-03-1.79e-01-0.1557
9517SPTLC2A001-C-108HumanColorectumFAP9.54e-11-3.41e-01-0.0272
9517SPTLC2A002-C-205HumanColorectumFAP1.04e-15-2.93e-01-0.1236
9517SPTLC2A015-C-005HumanColorectumFAP3.22e-03-2.52e-01-0.0336
9517SPTLC2A015-C-006HumanColorectumFAP4.49e-13-4.07e-01-0.0994
9517SPTLC2A015-C-106HumanColorectumFAP6.02e-06-2.95e-01-0.0511
9517SPTLC2A002-C-114HumanColorectumFAP1.56e-13-3.17e-01-0.1561
9517SPTLC2A015-C-104HumanColorectumFAP1.29e-15-3.90e-01-0.1899
9517SPTLC2A001-C-014HumanColorectumFAP5.52e-09-3.05e-010.0135
9517SPTLC2A002-C-016HumanColorectumFAP7.20e-15-3.52e-010.0521
9517SPTLC2A015-C-002HumanColorectumFAP1.71e-10-4.42e-01-0.0763
9517SPTLC2A001-C-203HumanColorectumFAP5.77e-06-2.55e-01-0.0481
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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
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
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
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
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
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:0009896ColorectumADpositive regulation of catabolic process180/3918492/187234.33e-161.94e-13180
GO:0031331ColorectumADpositive regulation of cellular catabolic process156/3918427/187234.68e-141.05e-11156
GO:0010506ColorectumADregulation of autophagy111/3918317/187233.57e-092.35e-07111
GO:0016236ColorectumADmacroautophagy103/3918291/187236.76e-094.15e-07103
GO:0006066ColorectumADalcohol metabolic process106/3918353/187233.02e-055.57e-04106
GO:0061912ColorectumADselective autophagy29/391868/187234.20e-057.39e-0429
GO:0016241ColorectumADregulation of macroautophagy50/3918141/187234.55e-057.92e-0450
GO:0010508ColorectumADpositive regulation of autophagy43/3918124/187232.64e-043.27e-0343
GO:0006644ColorectumADphospholipid metabolic process101/3918383/187235.80e-033.67e-02101
GO:00098962ColorectumMSSpositive regulation of catabolic process163/3467492/187233.10e-159.22e-13163
GO:00313312ColorectumMSSpositive regulation of cellular catabolic process140/3467427/187237.02e-131.33e-10140
GO:00162362ColorectumMSSmacroautophagy93/3467291/187232.08e-081.17e-0693
GO:00105062ColorectumMSSregulation of autophagy95/3467317/187234.36e-071.71e-0595
GO:00619122ColorectumMSSselective autophagy27/346768/187233.68e-057.09e-0427
GO:00162412ColorectumMSSregulation of macroautophagy44/3467141/187231.88e-042.64e-0344
GO:00060662ColorectumMSSalcohol metabolic process92/3467353/187232.57e-043.46e-0392
GO:00098964ColorectumFAPpositive regulation of catabolic process126/2622492/187233.76e-122.56e-09126
GO:00313314ColorectumFAPpositive regulation of cellular catabolic process110/2622427/187236.09e-112.19e-08110
GO:00105063ColorectumFAPregulation of autophagy80/2622317/187236.43e-084.54e-0680
GO:00162363ColorectumFAPmacroautophagy70/2622291/187232.73e-061.02e-0470
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa04071ColorectumADSphingolipid signaling pathway43/2092121/84654.83e-032.28e-021.45e-0243
hsa040711ColorectumADSphingolipid signaling pathway43/2092121/84654.83e-032.28e-021.45e-0243
hsa040714ColorectumFAPSphingolipid signaling pathway34/1404121/84659.53e-045.22e-033.17e-0334
hsa040715ColorectumFAPSphingolipid signaling pathway34/1404121/84659.53e-045.22e-033.17e-0334
hsa040716ColorectumCRCSphingolipid signaling pathway30/1091121/84652.49e-043.09e-032.09e-0330
hsa040717ColorectumCRCSphingolipid signaling pathway30/1091121/84652.49e-043.09e-032.09e-0330
hsa0407116EsophagusESCCSphingolipid signaling pathway85/4205121/84653.04e-061.73e-058.84e-0685
hsa006003EsophagusESCCSphingolipid metabolism36/420553/84655.41e-031.36e-026.99e-0336
hsa0407117EsophagusESCCSphingolipid signaling pathway85/4205121/84653.04e-061.73e-058.84e-0685
hsa0060012EsophagusESCCSphingolipid metabolism36/420553/84655.41e-031.36e-026.99e-0336
hsa040718LiverHCCSphingolipid signaling pathway72/4020121/84655.01e-031.47e-028.18e-0372
hsa00600LiverHCCSphingolipid metabolism34/402053/84651.06e-022.71e-021.51e-0234
hsa0407111LiverHCCSphingolipid signaling pathway72/4020121/84655.01e-031.47e-028.18e-0372
hsa006001LiverHCCSphingolipid metabolism34/402053/84651.06e-022.71e-021.51e-0234
hsa040719LungIACSphingolipid signaling pathway28/1053121/84657.30e-046.08e-034.04e-0328
hsa0407112LungIACSphingolipid signaling pathway28/1053121/84657.30e-046.08e-034.04e-0328
hsa0407114Oral cavityOSCCSphingolipid signaling pathway82/3704121/84656.97e-085.08e-072.58e-0782
hsa006002Oral cavityOSCCSphingolipid metabolism33/370453/84655.00e-031.20e-026.13e-0333
hsa0407115Oral cavityOSCCSphingolipid signaling pathway82/3704121/84656.97e-085.08e-072.58e-0782
hsa0060011Oral cavityOSCCSphingolipid metabolism33/370453/84655.00e-031.20e-026.13e-0333
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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
SPTLC2SNVMissense_Mutationnovelc.637N>Ap.Leu213Metp.L213MO15270protein_codingtolerated(0.11)benign(0.213)TCGA-A1-A0SI-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
SPTLC2SNVMissense_Mutationc.1627N>Tp.Arg543Trpp.R543WO15270protein_codingdeleterious(0)possibly_damaging(0.634)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
SPTLC2SNVMissense_Mutationnovelc.841A>Gp.Lys281Glup.K281EO15270protein_codingdeleterious(0.03)possibly_damaging(0.479)TCGA-AR-A5QQ-01Breastbreast invasive carcinomaFemale>=65III/IVChemotherapycarboplatinPD
SPTLC2SNVMissense_Mutationc.509N>Gp.Val170Glyp.V170GO15270protein_codingdeleterious(0)possibly_damaging(0.71)TCGA-BH-A0DL-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanCR
SPTLC2SNVMissense_Mutationc.1363N>Cp.Glu455Glnp.E455QO15270protein_codingtolerated(0.5)benign(0.129)TCGA-BH-A0DZ-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydocetaxelSD
SPTLC2SNVMissense_Mutationc.1588G>Ap.Glu530Lysp.E530KO15270protein_codingtolerated(0.12)benign(0.077)TCGA-D8-A27G-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
SPTLC2SNVMissense_Mutationnovelc.1489N>Ap.Gly497Argp.G497RO15270protein_codingdeleterious(0)probably_damaging(0.999)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
SPTLC2SNVMissense_Mutationrs763898397c.1628N>Ap.Arg543Glnp.R543QO15270protein_codingdeleterious(0.04)benign(0.086)TCGA-C5-A1BM-01Cervixcervical & endocervical cancerFemale>=65I/IIUnknownUnknownSD
SPTLC2deletionFrame_Shift_Delnovelc.395_407delACAACTGGAATCGp.Asp132GlyfsTer31p.D132Gfs*31O15270protein_codingTCGA-FU-A23L-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
SPTLC2SNVMissense_Mutationc.331T>Gp.Phe111Valp.F111VO15270protein_codingdeleterious(0)probably_damaging(0.945)TCGA-A6-3809-01Colorectumcolon 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
9517SPTLC2ENZYMEinhibitor178103276MYRIOCIN
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