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: SND1

Gene summary for SND1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

SND1

Gene ID

27044

Gene namestaphylococcal nuclease and tudor domain containing 1
Gene AliasTDRD11
Cytomap7q32.1
Gene Typeprotein-coding
GO ID

GO:0001503

UniProtAcc

A0A140VK49


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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
27044SND1CCI_2HumanCervixCC8.64e-036.55e-010.5249
27044SND1HTA11_1391_2000001011HumanColorectumAD9.28e-066.99e-01-0.059
27044SND1HTA11_99999970781_79442HumanColorectumMSS6.80e-044.55e-010.294
27044SND1HTA11_99999965062_69753HumanColorectumMSI-H6.61e-241.46e+000.3487
27044SND1HTA11_99999965104_69814HumanColorectumMSS3.76e-181.15e+000.281
27044SND1HTA11_99999971662_82457HumanColorectumMSS9.93e-231.21e+000.3859
27044SND1A015-C-203HumanColorectumFAP1.12e-35-5.97e-01-0.1294
27044SND1A015-C-204HumanColorectumFAP9.28e-09-3.57e-01-0.0228
27044SND1A014-C-040HumanColorectumFAP9.61e-06-5.01e-01-0.1184
27044SND1A002-C-201HumanColorectumFAP2.28e-14-3.46e-010.0324
27044SND1A001-C-119HumanColorectumFAP4.93e-18-7.17e-01-0.1557
27044SND1A001-C-108HumanColorectumFAP3.74e-21-5.22e-01-0.0272
27044SND1A002-C-205HumanColorectumFAP9.20e-32-5.91e-01-0.1236
27044SND1A001-C-104HumanColorectumFAP1.07e-03-3.51e-010.0184
27044SND1A015-C-005HumanColorectumFAP1.04e-05-3.44e-01-0.0336
27044SND1A015-C-006HumanColorectumFAP1.96e-20-5.21e-01-0.0994
27044SND1A015-C-106HumanColorectumFAP1.30e-17-3.92e-01-0.0511
27044SND1A002-C-114HumanColorectumFAP8.47e-29-6.87e-01-0.1561
27044SND1A015-C-104HumanColorectumFAP7.76e-40-6.97e-01-0.1899
27044SND1A001-C-014HumanColorectumFAP7.20e-19-4.33e-010.0135
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
CervixThe 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.CC: Cervix cancer
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
N_HPV: HPV-infected normal cervix
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
SkinThe 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.AK: Actinic keratosis
cSCC: Cutaneous squamous cell carcinoma
SCCIS:squamous cell carcinoma in situ
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:00064029CervixCCmRNA catabolic process56/2311232/187234.81e-071.83e-0556
GO:00064019CervixCCRNA catabolic process62/2311278/187232.18e-066.56e-0562
GO:00016497CervixCCosteoblast differentiation47/2311229/187232.88e-043.11e-0347
GO:00467008CervixCCheterocycle catabolic process80/2311445/187233.23e-043.42e-0380
GO:00346559CervixCCnucleobase-containing compound catabolic process74/2311407/187233.77e-043.88e-0374
GO:00442709CervixCCcellular nitrogen compound catabolic process79/2311451/187237.80e-046.91e-0379
GO:00015037CervixCCossification71/2311408/187231.67e-031.28e-0271
GO:00194398CervixCCaromatic compound catabolic process79/2311467/187232.14e-031.54e-0279
GO:19013618CervixCCorganic cyclic compound catabolic process80/2311495/187236.77e-033.72e-0280
GO:0006401ColorectumADRNA catabolic process102/3918278/187238.64e-106.76e-08102
GO:0044270ColorectumADcellular nitrogen compound catabolic process147/3918451/187233.35e-092.23e-07147
GO:0046700ColorectumADheterocycle catabolic process145/3918445/187234.37e-092.84e-07145
GO:0006402ColorectumADmRNA catabolic process87/3918232/187234.40e-092.84e-0787
GO:0034655ColorectumADnucleobase-containing compound catabolic process133/3918407/187231.56e-089.12e-07133
GO:0019439ColorectumADaromatic compound catabolic process146/3918467/187237.48e-083.84e-06146
GO:1901361ColorectumADorganic cyclic compound catabolic process153/3918495/187238.23e-084.18e-06153
GO:0001649ColorectumADosteoblast differentiation70/3918229/187233.59e-044.18e-0370
GO:0001503ColorectumADossification106/3918408/187237.68e-034.64e-02106
GO:00064012ColorectumMSSRNA catabolic process102/3467278/187235.07e-131.02e-10102
GO:00064022ColorectumMSSmRNA catabolic process89/3467232/187238.70e-131.60e-1089
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa0520325EsophagusESCCViral carcinogenesis137/4205204/84652.47e-071.88e-069.62e-07137
hsa0520335EsophagusESCCViral carcinogenesis137/4205204/84652.47e-071.88e-069.62e-07137
hsa05203LiverCirrhoticViral carcinogenesis76/2530204/84651.34e-024.20e-022.59e-0276
hsa052031LiverCirrhoticViral carcinogenesis76/2530204/84651.34e-024.20e-022.59e-0276
hsa052032LiverHCCViral carcinogenesis117/4020204/84652.68e-038.98e-035.00e-03117
hsa052033LiverHCCViral carcinogenesis117/4020204/84652.68e-038.98e-035.00e-03117
hsa052034LungIACViral carcinogenesis43/1053204/84653.02e-043.07e-032.04e-0343
hsa0520311LungIACViral carcinogenesis43/1053204/84653.02e-043.07e-032.04e-0343
hsa0520321LungAISViral carcinogenesis37/961204/84652.49e-031.49e-029.55e-0337
hsa0520331LungAISViral carcinogenesis37/961204/84652.49e-031.49e-029.55e-0337
hsa052038Oral cavityOSCCViral carcinogenesis124/3704204/84655.57e-073.28e-061.67e-06124
hsa0520314Oral cavityOSCCViral carcinogenesis124/3704204/84655.57e-073.28e-061.67e-06124
hsa0520324Oral cavityLPViral carcinogenesis90/2418204/84651.20e-061.38e-058.89e-0690
hsa0520334Oral cavityLPViral carcinogenesis90/2418204/84651.20e-061.38e-058.89e-0690
hsa0520342Oral cavityEOLPViral carcinogenesis55/1218204/84651.54e-061.34e-057.92e-0655
hsa0520351Oral cavityEOLPViral carcinogenesis55/1218204/84651.54e-061.34e-057.92e-0655
hsa0520361Oral cavityNEOLPViral carcinogenesis56/1112204/84652.90e-085.34e-073.36e-0756
hsa0520371Oral cavityNEOLPViral carcinogenesis56/1112204/84652.90e-085.34e-073.36e-0756
hsa052037ProstateBPHViral carcinogenesis69/1718204/84653.40e-062.87e-051.78e-0569
hsa0520313ProstateBPHViral carcinogenesis69/1718204/84653.40e-062.87e-051.78e-0569
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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
SND1TREGEsophagusADJLINC00324,ZNF292,MBLAC2, etc.3.19e-02The 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.
SND1TREGEsophagusESCCLINC00324,ZNF292,MBLAC2, etc.1.33e-01The 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.
∗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
SND1SNVMissense_Mutationc.2662N>Tp.Ala888Serp.A888SQ7KZF4protein_codingtolerated(0.8)benign(0.013)TCGA-A2-A0ST-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamycinSD
SND1SNVMissense_Mutationc.2149N>Tp.Asp717Tyrp.D717YQ7KZF4protein_codingdeleterious(0.04)possibly_damaging(0.686)TCGA-D8-A1JA-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapyadriamycinPD
SND1SNVMissense_Mutationc.829N>Gp.Ile277Valp.I277VQ7KZF4protein_codingtolerated(0.38)benign(0.074)TCGA-E2-A14R-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinPD
SND1deletionFrame_Shift_Delc.752delTp.Phe251SerfsTer39p.F251Sfs*39Q7KZF4protein_codingTCGA-A8-A09Z-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
SND1insertionIn_Frame_Insnovelc.2711_2712insTCATTCCTTTTTATGGCTAAGGGAGAGCTCTGGp.Asp904_Glu905insHisSerPheLeuTrpLeuArgGluSerSerGlyp.D904_E905insHSFLWLRESSGQ7KZF4protein_codingTCGA-AO-A0J4-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
SND1insertionFrame_Shift_Insnovelc.2713_2714insCTTACCTp.Glu905AlafsTer42p.E905Afs*42Q7KZF4protein_codingTCGA-AO-A0J4-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
SND1SNVMissense_Mutationnovelc.2060T>Gp.Val687Glyp.V687GQ7KZF4protein_codingdeleterious(0)probably_damaging(0.955)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
SND1SNVMissense_Mutationc.241N>Gp.Pro81Alap.P81AQ7KZF4protein_codingdeleterious(0.04)benign(0.012)TCGA-C5-A1BQ-01Cervixcervical & endocervical cancerFemale>=65III/IVChemotherapycisplatinCR
SND1SNVMissense_Mutationc.112N>Gp.Gln38Glup.Q38EQ7KZF4protein_codingtolerated(0.11)benign(0.222)TCGA-IR-A3LH-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
SND1SNVMissense_Mutationc.835N>Tp.His279Tyrp.H279YQ7KZF4protein_codingdeleterious(0.04)possibly_damaging(0.737)TCGA-JW-A5VL-01Cervixcervical & endocervical cancerFemale<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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