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: PSMD5-AS1

Gene summary for PSMD5-AS1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

PSMD5-AS1

Gene ID

253039

Gene namecutA divalent cation tolerance like, pseudogene
Gene AliasPSMD5-AS1
Cytomap9q33.2
Gene Typepseudo
GO ID

NA

UniProtAcc

NA


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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
253039PSMD5-AS1P1T-EHumanEsophagusESCC1.97e-237.72e-010.0875
253039PSMD5-AS1P2T-EHumanEsophagusESCC6.31e-487.35e-010.1177
253039PSMD5-AS1P4T-EHumanEsophagusESCC2.81e-132.94e-010.1323
253039PSMD5-AS1P5T-EHumanEsophagusESCC3.97e-041.29e-010.1327
253039PSMD5-AS1P8T-EHumanEsophagusESCC4.17e-051.71e-010.0889
253039PSMD5-AS1P9T-EHumanEsophagusESCC3.91e-274.91e-010.1131
253039PSMD5-AS1P10T-EHumanEsophagusESCC1.61e-325.39e-010.116
253039PSMD5-AS1P11T-EHumanEsophagusESCC1.72e-042.04e-010.1426
253039PSMD5-AS1P12T-EHumanEsophagusESCC4.16e-223.87e-010.1122
253039PSMD5-AS1P15T-EHumanEsophagusESCC1.55e-173.57e-010.1149
253039PSMD5-AS1P16T-EHumanEsophagusESCC5.03e-375.79e-010.1153
253039PSMD5-AS1P17T-EHumanEsophagusESCC2.14e-093.54e-010.1278
253039PSMD5-AS1P19T-EHumanEsophagusESCC6.53e-043.10e-010.1662
253039PSMD5-AS1P20T-EHumanEsophagusESCC4.80e-173.65e-010.1124
253039PSMD5-AS1P21T-EHumanEsophagusESCC2.05e-071.79e-010.1617
253039PSMD5-AS1P22T-EHumanEsophagusESCC6.62e-203.28e-010.1236
253039PSMD5-AS1P23T-EHumanEsophagusESCC2.37e-133.00e-010.108
253039PSMD5-AS1P24T-EHumanEsophagusESCC5.00e-173.60e-010.1287
253039PSMD5-AS1P26T-EHumanEsophagusESCC1.62e-132.56e-010.1276
253039PSMD5-AS1P27T-EHumanEsophagusESCC4.05e-325.07e-010.1055
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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
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
∗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
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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
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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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