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: SF3B4

Gene summary for SF3B4

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

SF3B4

Gene ID

10262

Gene namesplicing factor 3b subunit 4
Gene AliasAFD1
Cytomap1q21.2
Gene Typeprotein-coding
GO ID

GO:0000375

UniProtAcc

B3KUJ0


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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
10262SF3B4SYSMH2HumanOral cavityOSCC1.72e-216.98e-010.2326
10262SF3B4SYSMH3HumanOral cavityOSCC1.92e-256.73e-010.2442
10262SF3B4SYSMH4HumanOral cavityOSCC2.03e-021.51e-010.1226
10262SF3B4SYSMH5HumanOral cavityOSCC5.09e-114.32e-010.0647
10262SF3B4SYSMH6HumanOral cavityOSCC1.67e-052.57e-010.1275
10262SF3B4P4_S8_cSCCHumanSkincSCC3.73e-028.16e-02-0.3095
10262SF3B4P1_cSCCHumanSkincSCC8.70e-187.75e-010.0292
10262SF3B4P2_cSCCHumanSkincSCC6.70e-124.98e-01-0.024
10262SF3B4P4_cSCCHumanSkincSCC2.44e-146.47e-01-0.00290000000000005
10262SF3B4P10_cSCCHumanSkincSCC4.68e-227.11e-010.1017
10262SF3B4cSCC_p7HumanSkincSCC1.82e-03-9.09e-02-0.2332
10262SF3B4male-WTAHumanThyroidPTC1.16e-403.59e-010.1037
10262SF3B4PTC01HumanThyroidPTC3.90e-072.79e-020.1899
10262SF3B4PTC03HumanThyroidPTC1.45e-033.65e-020.1784
10262SF3B4PTC04HumanThyroidPTC1.83e-152.91e-020.1927
10262SF3B4PTC05HumanThyroidPTC7.18e-144.69e-010.2065
10262SF3B4PTC06HumanThyroidPTC4.26e-223.93e-010.2057
10262SF3B4PTC07HumanThyroidPTC3.33e-262.42e-010.2044
10262SF3B4ATC09HumanThyroidATC1.30e-032.35e-020.2871
10262SF3B4ATC11HumanThyroidATC9.99e-032.25e-010.3386
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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
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
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
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:0008380ColorectumADRNA splicing169/3918434/187233.59e-182.04e-15169
GO:0000377ColorectumADRNA splicing, via transesterification reactions with bulged adenosine as nucleophile130/3918320/187235.88e-162.16e-13130
GO:0000398ColorectumADmRNA splicing, via spliceosome130/3918320/187235.88e-162.16e-13130
GO:0000375ColorectumADRNA splicing, via transesterification reactions131/3918324/187237.11e-162.22e-13131
GO:1903311ColorectumADregulation of mRNA metabolic process117/3918288/187231.69e-144.23e-12117
GO:0043484ColorectumADregulation of RNA splicing70/3918148/187236.47e-131.16e-1070
GO:0048024ColorectumADregulation of mRNA splicing, via spliceosome50/3918101/187231.62e-101.56e-0850
GO:0050684ColorectumADregulation of mRNA processing61/3918137/187234.23e-103.58e-0861
GO:1903313ColorectumADpositive regulation of mRNA metabolic process44/3918118/187233.20e-055.87e-0444
GO:0033120ColorectumADpositive regulation of RNA splicing19/391837/187234.08e-057.26e-0419
GO:0048026ColorectumADpositive regulation of mRNA splicing, via spliceosome12/391822/187235.38e-045.74e-0312
GO:0008380111EsophagusESCCRNA splicing336/8552434/187231.74e-423.67e-39336
GO:0000375111EsophagusESCCRNA splicing, via transesterification reactions248/8552324/187233.05e-301.49e-27248
GO:0000377111EsophagusESCCRNA splicing, via transesterification reactions with bulged adenosine as nucleophile244/8552320/187232.52e-291.07e-26244
GO:0000398111EsophagusESCCmRNA splicing, via spliceosome244/8552320/187232.52e-291.07e-26244
GO:1903311110EsophagusESCCregulation of mRNA metabolic process210/8552288/187233.25e-215.56e-19210
GO:0043484111EsophagusESCCregulation of RNA splicing116/8552148/187233.18e-162.38e-14116
GO:0050684110EsophagusESCCregulation of mRNA processing109/8552137/187233.51e-162.59e-14109
GO:0048024111EsophagusESCCregulation of mRNA splicing, via spliceosome78/8552101/187238.72e-112.66e-0978
GO:190331316EsophagusESCCpositive regulation of mRNA metabolic process87/8552118/187235.10e-101.32e-0887
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa0304027EsophagusESCCSpliceosome128/4205217/84653.31e-038.79e-034.50e-03128
hsa0304037EsophagusESCCSpliceosome128/4205217/84653.31e-038.79e-034.50e-03128
hsa030407LiverCirrhoticSpliceosome102/2530217/84655.69e-089.47e-075.84e-07102
hsa0304012LiverCirrhoticSpliceosome102/2530217/84655.69e-089.47e-075.84e-07102
hsa0304022LiverHCCSpliceosome122/4020217/84655.55e-031.60e-028.91e-03122
hsa0304032LiverHCCSpliceosome122/4020217/84655.55e-031.60e-028.91e-03122
hsa0304016Oral cavityOSCCSpliceosome123/3704217/84657.21e-052.74e-041.40e-04123
hsa0304017Oral cavityOSCCSpliceosome123/3704217/84657.21e-052.74e-041.40e-04123
hsa0304026Oral cavityLPSpliceosome106/2418217/84651.30e-102.40e-091.55e-09106
hsa0304036Oral cavityLPSpliceosome106/2418217/84651.30e-102.40e-091.55e-09106
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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
SF3B4SNVMissense_Mutationc.1061G>Tp.Arg354Leup.R354LQ15427protein_codingdeleterious(0.01)benign(0.048)TCGA-A2-A0CW-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyanastrozoleSD
SF3B4SNVMissense_Mutationc.360N>Gp.Phe120Leup.F120LQ15427protein_codingdeleterious(0.03)probably_damaging(0.998)TCGA-C8-A12P-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
SF3B4insertionFrame_Shift_Insrs782357237c.1060dupCp.Arg354ProfsTer132p.R354Pfs*132Q15427protein_codingTCGA-D8-A13Y-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
SF3B4SNVMissense_Mutationnovelc.718N>Tp.Pro240Serp.P240SQ15427protein_codingtolerated(0.19)benign(0.009)TCGA-HM-A6W2-06Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinSD
SF3B4SNVMissense_Mutationc.869A>Gp.His290Argp.H290RQ15427protein_codingtolerated(0.3)benign(0.007)TCGA-A6-2686-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownSD
SF3B4SNVMissense_Mutationnovelc.1249N>Ap.Pro417Thrp.P417TQ15427protein_codingdeleterious_low_confidence(0)probably_damaging(0.981)TCGA-AA-3947-01Colorectumcolon adenocarcinomaFemale<65I/IIUnknownUnknownSD
SF3B4SNVMissense_Mutationnovelc.1259G>Ap.Gly420Aspp.G420DQ15427protein_codingdeleterious_low_confidence(0)benign(0.029)TCGA-AA-3949-01Colorectumcolon adenocarcinomaFemale>=65III/IVUnknownUnknownSD
SF3B4SNVMissense_Mutationc.578G>Ap.Arg193Glnp.R193QQ15427protein_codingdeleterious(0.05)probably_damaging(0.95)TCGA-AA-A00N-01Colorectumcolon adenocarcinomaMale>=65I/IIUnknownUnknownPD
SF3B4SNVMissense_Mutationc.1120N>Tp.Arg374Cysp.R374CQ15427protein_codingdeleterious_low_confidence(0.01)possibly_damaging(0.725)TCGA-D5-6540-01Colorectumcolon adenocarcinomaMale>=65I/IIUnknownUnknownSD
SF3B4SNVMissense_Mutationc.940N>Tp.His314Tyrp.H314YQ15427protein_codingdeleterious(0)benign(0.066)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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