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: SMA4

Gene summary for SMA4

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

SMA4

Gene ID

6606

Gene namesurvival of motor neuron 1, telomeric
Gene AliasBCD541
Cytomap5q13.2
Gene Typeprotein-coding
GO ID

GO:0000245

UniProtAcc

Q16637


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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
6606SMA4HCC1HumanLiverHCC3.12e-032.64e+000.5336
6606SMA4HCC2HumanLiverHCC9.74e-223.08e+000.5341
6606SMA4HCC5HumanLiverHCC5.65e-041.27e+000.4932
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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
∗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:00104989BreastPrecancerproteasomal protein catabolic process58/1080490/187231.54e-078.05e-0658
GO:001049814BreastIDCproteasomal protein catabolic process75/1434490/187235.59e-094.41e-0775
GO:001049824BreastDCISproteasomal protein catabolic process75/1390490/187231.44e-091.40e-0775
GO:001049816EndometriumAEHproteasomal protein catabolic process108/2100490/187232.73e-124.67e-10108
GO:001049817EndometriumEECproteasomal protein catabolic process112/2168490/187236.99e-131.40e-10112
GO:001049826EsophagusHGINproteasomal protein catabolic process139/2587490/187231.20e-173.41e-15139
GO:0010498111EsophagusESCCproteasomal protein catabolic process369/8552490/187231.13e-411.80e-38369
GO:001049812LiverCirrhoticproteasomal protein catabolic process216/4634490/187232.52e-219.29e-19216
GO:001049822LiverHCCproteasomal protein catabolic process351/7958490/187236.92e-401.46e-36351
GO:001049820Oral cavityOSCCproteasomal protein catabolic process336/7305490/187235.45e-418.63e-38336
GO:0010498110Oral cavityLPproteasomal protein catabolic process224/4623490/187239.57e-254.00e-22224
GO:001049818ProstateBPHproteasomal protein catabolic process153/3107490/187234.13e-167.51e-14153
GO:001049819ProstateTumorproteasomal protein catabolic process158/3246490/187233.05e-166.76e-14158
GO:001049827SkinAKproteasomal protein catabolic process97/1910490/187239.65e-111.54e-0897
GO:001049828SkincSCCproteasomal protein catabolic process243/4864490/187237.85e-304.10e-27243
GO:0010498113ThyroidPTCproteasomal protein catabolic process297/5968490/187234.58e-409.63e-37297
GO:001049832ThyroidATCproteasomal protein catabolic process309/6293490/187231.78e-411.13e-37309
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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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