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: CASK

Gene summary for CASK

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

CASK

Gene ID

8573

Gene namecalcium/calmodulin dependent serine protein kinase
Gene AliasCAGH39
CytomapXp11.4
Gene Typeprotein-coding
GO ID

GO:0001505

UniProtAcc

O14936


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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
8573CASKCCI_1HumanCervixCC3.11e-181.26e+000.528
8573CASKCCI_2HumanCervixCC4.38e-131.47e+000.5249
8573CASKCCI_3HumanCervixCC7.57e-171.17e+000.516
8573CASKHTA11_3410_2000001011HumanColorectumAD8.58e-12-3.56e-010.0155
8573CASKHTA11_2487_2000001011HumanColorectumSER1.71e-04-3.09e-01-0.1808
8573CASKHTA11_347_2000001011HumanColorectumAD6.34e-085.12e-01-0.1954
8573CASKHTA11_5212_2000001011HumanColorectumAD2.28e-08-6.10e-01-0.2061
8573CASKHTA11_5216_2000001011HumanColorectumSER1.40e-05-6.05e-01-0.1462
8573CASKHTA11_8622_2000001021HumanColorectumSER9.09e-04-5.47e-010.0528
8573CASKHTA11_99999970781_79442HumanColorectumMSS3.02e-09-3.84e-010.294
8573CASKHTA11_99999965104_69814HumanColorectumMSS2.41e-201.25e+000.281
8573CASKA015-C-203HumanColorectumFAP4.08e-39-5.54e-01-0.1294
8573CASKA015-C-204HumanColorectumFAP1.93e-04-3.55e-01-0.0228
8573CASKA014-C-040HumanColorectumFAP4.95e-06-5.88e-01-0.1184
8573CASKA002-C-201HumanColorectumFAP2.55e-11-4.03e-010.0324
8573CASKA002-C-203HumanColorectumFAP5.46e-03-1.67e-010.2786
8573CASKA001-C-119HumanColorectumFAP3.33e-10-5.57e-01-0.1557
8573CASKA001-C-108HumanColorectumFAP1.60e-16-2.73e-01-0.0272
8573CASKA002-C-205HumanColorectumFAP5.41e-29-6.62e-01-0.1236
8573CASKA015-C-006HumanColorectumFAP6.23e-22-7.18e-01-0.0994
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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
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
GCThe 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.CAG: Chronic atrophic gastritis
CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
CSG: Chronic superficial gastritis
GC: Gastric cancer
SIM: Severe intestinal metaplasia
WIM: Wild intestinal metaplasia
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
∗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:004206010CervixCCwound healing109/2311422/187231.84e-141.57e-11109
GO:001081010CervixCCregulation of cell-substrate adhesion69/2311221/187238.57e-145.69e-1169
GO:00315898CervixCCcell-substrate adhesion96/2311363/187231.48e-138.85e-1196
GO:00506737CervixCCepithelial cell proliferation98/2311437/187232.01e-092.15e-0798
GO:00019528CervixCCregulation of cell-matrix adhesion40/2311128/187231.32e-081.04e-0640
GO:00071608CervixCCcell-matrix adhesion60/2311233/187231.58e-081.23e-0660
GO:00071626CervixCCnegative regulation of cell adhesion72/2311303/187232.36e-081.70e-0672
GO:00506787CervixCCregulation of epithelial cell proliferation83/2311381/187231.31e-076.42e-0683
GO:19030349CervixCCregulation of response to wounding44/2311167/187236.33e-072.31e-0544
GO:00610418CervixCCregulation of wound healing34/2311134/187232.70e-054.52e-0434
GO:00108122CervixCCnegative regulation of cell-substrate adhesion21/231168/187234.35e-056.66e-0421
GO:00436164CervixCCkeratinocyte proliferation15/231146/187232.70e-042.97e-0315
GO:00196939CervixCCribose phosphate metabolic process72/2311396/187234.49e-044.48e-0372
GO:00092599CervixCCribonucleotide metabolic process70/2311385/187235.35e-045.18e-0370
GO:00321022CervixCCnegative regulation of response to external stimulus75/2311420/187235.96e-045.61e-0375
GO:00108376CervixCCregulation of keratinocyte proliferation12/231135/187236.55e-046.05e-0312
GO:000915010CervixCCpurine ribonucleotide metabolic process66/2311368/187231.09e-039.07e-0366
GO:00171574CervixCCregulation of exocytosis39/2311202/187232.90e-031.93e-0239
GO:000616310CervixCCpurine nucleotide metabolic process67/2311396/187234.41e-032.69e-0267
GO:007252110CervixCCpurine-containing compound metabolic process69/2311416/187236.27e-033.54e-0269
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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
CASKSNVMissense_Mutationc.2668N>Gp.Ile890Valp.I890VO14936protein_codingtolerated(1)benign(0)TCGA-A1-A0SD-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
CASKSNVMissense_Mutationc.1870G>Cp.Asp624Hisp.D624HO14936protein_codingdeleterious(0)probably_damaging(0.965)TCGA-A2-A04R-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapytaxolSD
CASKSNVMissense_Mutationc.1727N>Tp.Ser576Leup.S576LO14936protein_codingtolerated(0.17)benign(0)TCGA-A2-A0YT-01Breastbreast invasive carcinomaFemale<65III/IVHormone TherapyarimidexSD
CASKSNVMissense_Mutationnovelc.527N>Gp.Ala176Glyp.A176GO14936protein_codingtolerated(0.25)benign(0.017)TCGA-A2-A4S1-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
CASKSNVMissense_Mutationc.847G>Ap.Ala283Thrp.A283TO14936protein_codingdeleterious(0.02)benign(0.098)TCGA-AO-A128-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
CASKSNVMissense_Mutationnovelc.1521G>Ap.Met507Ilep.M507IO14936protein_codingtolerated(0.25)benign(0.015)TCGA-BH-A2L8-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanCR
CASKSNVMissense_Mutationc.2454N>Gp.Ile818Metp.I818MO14936protein_codingdeleterious(0)probably_damaging(0.996)TCGA-C8-A26Y-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
CASKSNVMissense_Mutationc.1916N>Ap.Arg639Glnp.R639QO14936protein_codingtolerated(0.52)benign(0.313)TCGA-D8-A27G-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
CASKinsertionFrame_Shift_Insnovelc.14_15insGTTGGGGTTATTGTTACCTTGCATGTACCATAGACCATTTTTGAAACp.Asp5GlufsTer29p.D5Efs*29O14936protein_codingTCGA-AN-A0FX-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
CASKinsertionFrame_Shift_Insnovelc.1519dupAp.Met507AsnfsTer3p.M507Nfs*3O14936protein_codingTCGA-BH-A2L8-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanCR
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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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