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: PHF21A

Gene summary for PHF21A

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

PHF21A

Gene ID

51317

Gene namePHD finger protein 21A
Gene AliasBHC80
Cytomap11p11.2
Gene Typeprotein-coding
GO ID

GO:0000122

UniProtAcc

Q96BD5


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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
51317PHF21ACCI_1HumanCervixCC8.07e-075.98e-010.528
51317PHF21ACCI_2HumanCervixCC2.13e-036.55e-010.5249
51317PHF21ACCI_3HumanCervixCC9.78e-147.80e-010.516
51317PHF21ALZE4THumanEsophagusESCC1.32e-133.17e-010.0811
51317PHF21ALZE5THumanEsophagusESCC3.25e-022.44e-010.0514
51317PHF21ALZE8THumanEsophagusESCC6.47e-341.14e+000.067
51317PHF21ALZE24THumanEsophagusESCC3.59e-112.42e-010.0596
51317PHF21AP1T-EHumanEsophagusESCC1.31e-052.23e-010.0875
51317PHF21AP2T-EHumanEsophagusESCC2.48e-163.00e-010.1177
51317PHF21AP4T-EHumanEsophagusESCC1.64e-028.62e-020.1323
51317PHF21AP8T-EHumanEsophagusESCC4.00e-121.62e-010.0889
51317PHF21AP9T-EHumanEsophagusESCC2.32e-092.11e-010.1131
51317PHF21AP10T-EHumanEsophagusESCC2.10e-142.93e-010.116
51317PHF21AP11T-EHumanEsophagusESCC8.10e-063.66e-010.1426
51317PHF21AP12T-EHumanEsophagusESCC4.47e-152.43e-010.1122
51317PHF21AP15T-EHumanEsophagusESCC2.32e-133.15e-010.1149
51317PHF21AP16T-EHumanEsophagusESCC1.31e-111.51e-010.1153
51317PHF21AP17T-EHumanEsophagusESCC3.80e-032.02e-010.1278
51317PHF21AP20T-EHumanEsophagusESCC1.07e-142.94e-010.1124
51317PHF21AP21T-EHumanEsophagusESCC1.72e-058.50e-020.1617
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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
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:00063257CervixCCchromatin organization78/2311409/187235.40e-058.02e-0478
GO:000632517EsophagusESCCchromatin organization240/8552409/187236.52e-081.14e-06240
GO:00063255LiverNAFLDchromatin organization64/1882409/187232.31e-043.89e-0364
GO:000632511LiverHCCchromatin organization206/7958409/187237.23e-044.41e-03206
GO:00063256LungIACchromatin organization69/2061409/187232.01e-043.53e-0369
GO:000632512LungAISchromatin organization62/1849409/187234.24e-047.29e-0362
GO:000632510Oral cavityOSCCchromatin organization190/7305409/187231.17e-035.97e-03190
GO:000632515Oral cavityEOLPchromatin organization84/2218409/187232.68e-078.16e-0684
GO:000632521Oral cavityNEOLPchromatin organization70/2005409/187234.97e-056.83e-0470
GO:00063259ProstateBPHchromatin organization101/3107409/187231.52e-051.94e-04101
GO:000632514ProstateTumorchromatin organization104/3246409/187232.02e-052.62e-04104
GO:000632520ThyroidPTCchromatin organization183/5968409/187232.55e-085.70e-07183
GO:0006325110ThyroidATCchromatin organization189/6293409/187236.40e-081.13e-06189
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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
PHF21AMDSCsOral cavityADJST6GALNAC3,GOLGA1,PEX16, etc.1.06e-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.
PHF21ACD8TEXPOral cavityLPST6GALNAC3,GOLGA1,PEX16, etc.2.13e-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.
PHF21ANKOral cavityLPST6GALNAC3,GOLGA1,PEX16, etc.2.23e-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.
PHF21ATH17Oral cavityLPST6GALNAC3,GOLGA1,PEX16, etc.3.52e-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.
PHF21ATH17SkincSCCPIK3CD,GLG1,MYO5A, etc.1.53e-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.
PHF21ACD8TEREXSkinSCCISPIK3CD,GLG1,MYO5A, etc.2.23e-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.
∗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
PHF21ASNVMissense_Mutationnovelc.1907C>Tp.Ser636Phep.S636FQ96BD5protein_codingdeleterious(0.01)possibly_damaging(0.876)TCGA-3C-AALI-01Breastbreast invasive carcinomaFemale<65I/IIUnspecificPoly EComplete Response
PHF21ASNVMissense_Mutationc.985G>Cp.Glu329Glnp.E329QQ96BD5protein_codingtolerated(0.39)possibly_damaging(0.836)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
PHF21AinsertionFrame_Shift_Insnovelc.1708_1709insCTGCTTTCTCCTCCTCACCATACCTACCCATGGCATGCAGATTTp.Leu570ProfsTer22p.L570Pfs*22Q96BD5protein_codingTCGA-B6-A0IC-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
PHF21ASNVMissense_Mutationc.1033N>Ap.Glu345Lysp.E345KQ96BD5protein_codingtolerated(0.33)benign(0.023)TCGA-DS-A0VL-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
PHF21ASNVMissense_Mutationrs149898933c.2012C>Tp.Ala671Valp.A671VQ96BD5protein_codingtolerated_low_confidence(1)benign(0)TCGA-LP-A5U2-01Cervixcervical & endocervical cancerFemale<65III/IVUnknownUnknownSD
PHF21ASNVMissense_Mutationnovelc.817N>Cp.Thr273Prop.T273PQ96BD5protein_codingtolerated(0.2)benign(0)TCGA-A6-5665-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownPD
PHF21ASNVMissense_Mutationrs532473580c.928N>Gp.Thr310Alap.T310AQ96BD5protein_codingtolerated(0.3)benign(0)TCGA-AA-3672-01Colorectumcolon adenocarcinomaFemale>=65III/IVUnknownUnknownSD
PHF21ASNVMissense_Mutationrs370627435c.1868G>Ap.Arg623Hisp.R623HQ96BD5protein_codingtolerated(0.06)possibly_damaging(0.82)TCGA-AA-3947-01Colorectumcolon adenocarcinomaFemale<65I/IIUnknownUnknownSD
PHF21ASNVMissense_Mutationnovelc.890C>Tp.Thr297Metp.T297MQ96BD5protein_codingdeleterious(0.02)possibly_damaging(0.799)TCGA-AA-3949-01Colorectumcolon adenocarcinomaFemale>=65III/IVUnknownUnknownSD
PHF21ASNVMissense_Mutationc.1508N>Ap.Cys503Tyrp.C503YQ96BD5protein_codingdeleterious(0)probably_damaging(1)TCGA-G4-6588-01Colorectumcolon 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
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