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: SNX9

Gene summary for SNX9

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

SNX9

Gene ID

51429

Gene namesorting nexin 9
Gene AliasSDP1
Cytomap6q25.3
Gene Typeprotein-coding
GO ID

GO:0000278

UniProtAcc

Q9Y5X1


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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
51429SNX9HTA11_3410_2000001011HumanColorectumAD1.03e-06-4.06e-010.0155
51429SNX9HTA11_347_2000001011HumanColorectumAD1.48e-074.04e-01-0.1954
51429SNX9HTA11_411_2000001011HumanColorectumSER3.06e-049.10e-01-0.2602
51429SNX9HTA11_2112_2000001011HumanColorectumSER4.11e-025.69e-01-0.2196
51429SNX9HTA11_99999974143_84620HumanColorectumMSS1.06e-06-3.90e-010.3005
51429SNX9A015-C-203HumanColorectumFAP2.85e-30-4.71e-01-0.1294
51429SNX9A015-C-204HumanColorectumFAP3.35e-03-2.68e-01-0.0228
51429SNX9A002-C-201HumanColorectumFAP8.45e-07-3.26e-010.0324
51429SNX9A002-C-203HumanColorectumFAP2.48e-05-1.12e-010.2786
51429SNX9A001-C-119HumanColorectumFAP2.54e-02-2.31e-01-0.1557
51429SNX9A001-C-108HumanColorectumFAP6.39e-17-2.93e-01-0.0272
51429SNX9A002-C-205HumanColorectumFAP1.72e-13-3.62e-01-0.1236
51429SNX9A001-C-104HumanColorectumFAP2.67e-03-1.32e-010.0184
51429SNX9A015-C-006HumanColorectumFAP9.54e-09-4.47e-01-0.0994
51429SNX9A015-C-106HumanColorectumFAP3.34e-14-2.90e-01-0.0511
51429SNX9A002-C-114HumanColorectumFAP1.56e-11-4.07e-01-0.1561
51429SNX9A015-C-104HumanColorectumFAP6.79e-31-4.52e-01-0.1899
51429SNX9A001-C-014HumanColorectumFAP2.87e-12-1.77e-010.0135
51429SNX9A002-C-016HumanColorectumFAP2.14e-19-2.85e-010.0521
51429SNX9A015-C-002HumanColorectumFAP6.73e-06-2.05e-01-0.0763
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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
EndometriumThe 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.AEH: Atypical endometrial hyperplasia
EEC: Endometrioid 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:00325062ColorectumMSScytokinetic process14/346739/187237.79e-034.84e-0214
GO:0006509ColorectumMSSmembrane protein ectodomain proteolysis15/346743/187238.06e-034.91e-0215
GO:00070154ColorectumFAPactin filament organization125/2622442/187231.97e-153.03e-12125
GO:00098964ColorectumFAPpositive regulation of catabolic process126/2622492/187233.76e-122.56e-09126
GO:00421764ColorectumFAPregulation of protein catabolic process106/2622391/187235.00e-123.06e-09106
GO:00329704ColorectumFAPregulation of actin filament-based process105/2622397/187233.15e-111.38e-08105
GO:00313314ColorectumFAPpositive regulation of cellular catabolic process110/2622427/187236.09e-112.19e-08110
GO:00325353ColorectumFAPregulation of cellular component size99/2622383/187234.53e-101.16e-0799
GO:01100534ColorectumFAPregulation of actin filament organization75/2622278/187238.11e-091.10e-0675
GO:00329564ColorectumFAPregulation of actin cytoskeleton organization90/2622358/187231.20e-081.39e-0690
GO:00432544ColorectumFAPregulation of protein-containing complex assembly101/2622428/187235.18e-084.07e-06101
GO:19029034ColorectumFAPregulation of supramolecular fiber organization92/2622383/187238.48e-085.77e-0692
GO:00081544ColorectumFAPactin polymerization or depolymerization60/2622218/187231.15e-077.43e-0660
GO:00430873ColorectumFAPregulation of GTPase activity85/2622348/187231.20e-077.68e-0685
GO:00322714ColorectumFAPregulation of protein polymerization62/2622233/187232.64e-071.53e-0562
GO:19029054ColorectumFAPpositive regulation of supramolecular fiber organization57/2622209/187233.28e-071.83e-0557
GO:00457324ColorectumFAPpositive regulation of protein catabolic process61/2622231/187234.38e-072.35e-0561
GO:00514954ColorectumFAPpositive regulation of cytoskeleton organization60/2622226/187234.45e-072.37e-0560
GO:00300414ColorectumFAPactin filament polymerization53/2622191/187234.65e-072.46e-0553
GO:00313344ColorectumFAPpositive regulation of protein-containing complex assembly62/2622237/187235.03e-072.61e-0562
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa05132ColorectumADSalmonella infection102/2092249/84657.65e-091.28e-078.17e-08102
hsa051321ColorectumADSalmonella infection102/2092249/84657.65e-091.28e-078.17e-08102
hsa051322ColorectumSERSalmonella infection77/1580249/84651.56e-062.35e-051.71e-0577
hsa051323ColorectumSERSalmonella infection77/1580249/84651.56e-062.35e-051.71e-0577
hsa051328ColorectumFAPSalmonella infection67/1404249/84652.04e-052.52e-041.53e-0467
hsa051329ColorectumFAPSalmonella infection67/1404249/84652.04e-052.52e-041.53e-0467
hsa0513210ColorectumCRCSalmonella infection48/1091249/84652.43e-031.69e-021.15e-0248
hsa0513211ColorectumCRCSalmonella infection48/1091249/84652.43e-031.69e-021.15e-0248
hsa0513226EndometriumAEHSalmonella infection71/1197249/84651.69e-093.44e-082.52e-0871
hsa05132112EndometriumAEHSalmonella infection71/1197249/84651.69e-093.44e-082.52e-0871
hsa0513227EndometriumEECSalmonella infection71/1237249/84657.11e-091.30e-079.69e-0871
hsa0513236EndometriumEECSalmonella infection71/1237249/84657.11e-091.30e-079.69e-0871
hsa0513239EsophagusHGINSalmonella infection69/1383249/84653.02e-064.47e-053.55e-0569
hsa05132115EsophagusHGINSalmonella infection69/1383249/84653.02e-064.47e-053.55e-0569
hsa05132211EsophagusESCCSalmonella infection191/4205249/84656.51e-195.45e-172.79e-17191
hsa05132310EsophagusESCCSalmonella infection191/4205249/84656.51e-195.45e-172.79e-17191
hsa0513214LiverNAFLDSalmonella infection55/1043249/84658.48e-063.09e-042.49e-0455
hsa0513215LiverNAFLDSalmonella infection55/1043249/84658.48e-063.09e-042.49e-0455
hsa0513222LiverCirrhoticSalmonella infection121/2530249/84652.47e-105.13e-093.16e-09121
hsa0513232LiverCirrhoticSalmonella infection121/2530249/84652.47e-105.13e-093.16e-09121
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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
SNX9SNVMissense_Mutationnovelc.1123G>Ap.Ala375Thrp.A375TQ9Y5X1protein_codingdeleterious(0.01)benign(0.007)TCGA-A2-A0CP-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
SNX9SNVMissense_Mutationc.1597G>Cp.Asp533Hisp.D533HQ9Y5X1protein_codingdeleterious(0.04)probably_damaging(1)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
SNX9SNVMissense_Mutationc.28G>Ap.Asp10Asnp.D10NQ9Y5X1protein_codingtolerated(0.07)benign(0.092)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
SNX9insertionNonsense_Mutationnovelc.205_206insAGTTTAAATAGATTTTTTTAAGTGCATATCTCAGTTCp.Ser69Terp.S69*Q9Y5X1protein_codingTCGA-B6-A0IK-01Breastbreast invasive carcinomaFemale<65III/IVUnknownUnknownPD
SNX9SNVMissense_Mutationc.28N>Cp.Asp10Hisp.D10HQ9Y5X1protein_codingdeleterious(0)probably_damaging(0.949)TCGA-EK-A2RC-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
SNX9SNVMissense_Mutationc.1757N>Tp.Arg586Metp.R586MQ9Y5X1protein_codingdeleterious(0)possibly_damaging(0.857)TCGA-AA-3864-01Colorectumcolon adenocarcinomaMale>=65I/IIUnknownUnknownSD
SNX9SNVMissense_Mutationnovelc.1005G>Ap.Met335Ilep.M335IQ9Y5X1protein_codingdeleterious(0)possibly_damaging(0.793)TCGA-D5-6539-01Colorectumcolon adenocarcinomaFemale<65I/IIUnknownUnknownSD
SNX9SNVMissense_Mutationnovelc.700N>Tp.Ile234Phep.I234FQ9Y5X1protein_codingdeleterious(0)possibly_damaging(0.905)TCGA-AG-3726-01Colorectumrectum adenocarcinomaFemale<65I/IIUnknownUnknownSD
SNX9SNVMissense_Mutationnovelc.1205N>Gp.Val402Glyp.V402GQ9Y5X1protein_codingdeleterious(0)probably_damaging(0.939)TCGA-AG-A002-01Colorectumrectum adenocarcinomaMale<65I/IIUnknownUnknownSD
SNX9SNVMissense_Mutationnovelc.502N>Ap.Asp168Asnp.D168NQ9Y5X1protein_codingtolerated(0.45)possibly_damaging(0.678)TCGA-AG-A01N-01Colorectumrectum adenocarcinomaFemale>=65III/IVChemotherapycapecitabineSD
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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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