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: PHKB

Gene summary for PHKB

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

PHKB

Gene ID

5257

Gene namephosphorylase kinase regulatory subunit beta
Gene AliasPHKB
Cytomap16q12.1
Gene Typeprotein-coding
GO ID

GO:0005975

UniProtAcc

Q93100


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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
5257PHKBCRC-3-11773HumanColorectumCRC8.56e-12-4.28e-010.2564
5257PHKBLZE4THumanEsophagusESCC1.08e-238.74e-010.0811
5257PHKBLZE7THumanEsophagusESCC8.43e-065.64e-010.0667
5257PHKBLZE8THumanEsophagusESCC2.66e-038.07e-020.067
5257PHKBLZE24THumanEsophagusESCC1.02e-081.76e-010.0596
5257PHKBLZE21THumanEsophagusESCC1.19e-072.57e-010.0655
5257PHKBP1T-EHumanEsophagusESCC1.14e-083.55e-010.0875
5257PHKBP2T-EHumanEsophagusESCC2.02e-218.88e-020.1177
5257PHKBP4T-EHumanEsophagusESCC2.68e-215.45e-010.1323
5257PHKBP5T-EHumanEsophagusESCC5.37e-191.40e-010.1327
5257PHKBP8T-EHumanEsophagusESCC5.69e-305.04e-010.0889
5257PHKBP9T-EHumanEsophagusESCC2.23e-081.81e-010.1131
5257PHKBP10T-EHumanEsophagusESCC4.58e-243.58e-010.116
5257PHKBP11T-EHumanEsophagusESCC1.67e-123.32e-010.1426
5257PHKBP12T-EHumanEsophagusESCC1.70e-203.29e-010.1122
5257PHKBP15T-EHumanEsophagusESCC4.83e-195.20e-010.1149
5257PHKBP16T-EHumanEsophagusESCC8.37e-212.71e-010.1153
5257PHKBP17T-EHumanEsophagusESCC4.98e-093.06e-010.1278
5257PHKBP19T-EHumanEsophagusESCC1.82e-082.96e-010.1662
5257PHKBP20T-EHumanEsophagusESCC7.04e-195.45e-010.1124
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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
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:00060919CervixCCgeneration of precursor metabolites and energy105/2311490/187237.40e-096.61e-07105
GO:00159809CervixCCenergy derivation by oxidation of organic compounds74/2311318/187233.83e-082.53e-0674
GO:0006091ColorectumADgeneration of precursor metabolites and energy209/3918490/187233.17e-286.61e-25209
GO:0015980ColorectumADenergy derivation by oxidation of organic compounds143/3918318/187232.78e-222.49e-19143
GO:0044262ColorectumADcellular carbohydrate metabolic process87/3918283/187236.00e-051.01e-0387
GO:00060912ColorectumMSSgeneration of precursor metabolites and energy186/3467490/187231.14e-242.15e-21186
GO:00159802ColorectumMSSenergy derivation by oxidation of organic compounds131/3467318/187232.60e-212.70e-18131
GO:00060914ColorectumFAPgeneration of precursor metabolites and energy128/2622490/187235.58e-134.28e-10128
GO:00159804ColorectumFAPenergy derivation by oxidation of organic compounds85/2622318/187231.36e-092.77e-0785
GO:00442621ColorectumFAPcellular carbohydrate metabolic process66/2622283/187231.53e-054.01e-0466
GO:00060915ColorectumCRCgeneration of precursor metabolites and energy80/2078490/187232.55e-044.16e-0380
GO:00442622ColorectumCRCcellular carbohydrate metabolic process49/2078283/187231.06e-031.24e-0249
GO:0006091110EsophagusESCCgeneration of precursor metabolites and energy331/8552490/187233.86e-238.45e-21331
GO:0015980110EsophagusESCCenergy derivation by oxidation of organic compounds220/8552318/187231.20e-171.09e-15220
GO:00442626EsophagusESCCcellular carbohydrate metabolic process160/8552283/187231.43e-049.66e-04160
GO:00060917LiverNAFLDgeneration of precursor metabolites and energy84/1882490/187237.03e-073.95e-0584
GO:00442623LiverNAFLDcellular carbohydrate metabolic process55/1882283/187231.27e-066.01e-0555
GO:0005976LiverNAFLDpolysaccharide metabolic process24/1882107/187231.28e-042.46e-0324
GO:0044264LiverNAFLDcellular polysaccharide metabolic process22/188296/187231.73e-043.08e-0322
GO:0005977LiverNAFLDglycogen metabolic process18/188272/187232.09e-043.60e-0318
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa04922ColorectumADGlucagon signaling pathway41/2092107/84651.18e-037.75e-034.94e-0341
hsa049221ColorectumADGlucagon signaling pathway41/2092107/84651.18e-037.75e-034.94e-0341
hsa049224ColorectumMSSGlucagon signaling pathway39/1875107/84655.00e-043.45e-032.11e-0339
hsa04910ColorectumMSSInsulin signaling pathway43/1875137/84657.37e-032.84e-021.74e-0243
hsa049225ColorectumMSSGlucagon signaling pathway39/1875107/84655.00e-043.45e-032.11e-0339
hsa049101ColorectumMSSInsulin signaling pathway43/1875137/84657.37e-032.84e-021.74e-0243
hsa049226ColorectumFAPGlucagon signaling pathway32/1404107/84654.08e-043.10e-031.89e-0332
hsa049102ColorectumFAPInsulin signaling pathway36/1404137/84652.51e-031.18e-027.18e-0336
hsa049227ColorectumFAPGlucagon signaling pathway32/1404107/84654.08e-043.10e-031.89e-0332
hsa049103ColorectumFAPInsulin signaling pathway36/1404137/84652.51e-031.18e-027.18e-0336
hsa049104ColorectumCRCInsulin signaling pathway31/1091137/84651.07e-038.91e-036.03e-0331
hsa049228ColorectumCRCGlucagon signaling pathway24/1091107/84654.21e-032.47e-021.67e-0224
hsa049105ColorectumCRCInsulin signaling pathway31/1091137/84651.07e-038.91e-036.03e-0331
hsa049229ColorectumCRCGlucagon signaling pathway24/1091107/84654.21e-032.47e-021.67e-0224
hsa049109EsophagusESCCInsulin signaling pathway89/4205137/84651.97e-047.32e-043.75e-0489
hsa0492214EsophagusESCCGlucagon signaling pathway64/4205107/84652.18e-024.80e-022.46e-0264
hsa0491014EsophagusESCCInsulin signaling pathway89/4205137/84651.97e-047.32e-043.75e-0489
hsa0492215EsophagusESCCGlucagon signaling pathway64/4205107/84652.18e-024.80e-022.46e-0264
hsa049106LiverNAFLDInsulin signaling pathway29/1043137/84652.23e-032.46e-021.99e-0229
hsa0492210LiverNAFLDGlucagon signaling pathway24/1043107/84652.33e-032.46e-021.99e-0224
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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
PHKBSNVMissense_Mutationc.2428N>Tp.Val810Leup.V810LQ93100protein_codingtolerated(0.5)benign(0.139)TCGA-A2-A0CT-01Breastbreast invasive carcinomaFemale>=65I/IIChemotherapycytoxanSD
PHKBSNVMissense_Mutationnovelc.2435N>Cp.Leu812Prop.L812PQ93100protein_codingdeleterious(0)probably_damaging(0.99)TCGA-A2-A3XW-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamyicinCR
PHKBSNVMissense_Mutationc.1751N>Gp.Asp584Glyp.D584GQ93100protein_codingdeleterious(0)probably_damaging(0.998)TCGA-A8-A08R-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
PHKBSNVMissense_Mutationnovelc.2909N>Tp.Ser970Leup.S970LQ93100protein_codingdeleterious(0)probably_damaging(0.96)TCGA-BH-A0B6-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
PHKBSNVMissense_Mutationc.26N>Gp.Ala9Glyp.A9GQ93100protein_codingdeleterious_low_confidence(0.05)benign(0.015)TCGA-E2-A14S-01Breastbreast invasive carcinomaFemale>=65I/IIChemotherapycytoxanSD
PHKBinsertionFrame_Shift_Insnovelc.296_297insGp.Ala100CysfsTer6p.A100Cfs*6Q93100protein_codingTCGA-A8-A07U-01Breastbreast invasive carcinomaFemale>=65III/IVChemotherapy5-fluorouracilSD
PHKBinsertionIn_Frame_Insnovelc.298_299insTTCATGTTATATATGGATGGAATTp.Ala100delinsValHisValIleTyrGlyTrpAsnSerp.A100delinsVHVIYGWNSQ93100protein_codingTCGA-A8-A07U-01Breastbreast invasive carcinomaFemale>=65III/IVChemotherapy5-fluorouracilSD
PHKBdeletionFrame_Shift_Delc.664delGp.Glu222LysfsTer20p.E222Kfs*20Q93100protein_codingTCGA-EW-A2FV-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapydocetaxelSD
PHKBSNVMissense_Mutationc.1243N>Ap.Asp415Asnp.D415NQ93100protein_codingtolerated(0.12)benign(0.082)TCGA-EK-A2R7-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
PHKBSNVMissense_Mutationnovelc.3031N>Ap.Glu1011Lysp.E1011KQ93100protein_codingtolerated(0.12)benign(0.358)TCGA-JX-A3Q0-01Cervixcervical & endocervical cancerFemale<65III/IVUnknownUnknownSD
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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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