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: RSF1

Gene summary for RSF1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

RSF1

Gene ID

51773

Gene nameremodeling and spacing factor 1
Gene AliasHBXAP
Cytomap11q14.1
Gene Typeprotein-coding
GO ID

GO:0006139

UniProtAcc

Q05DG0


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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
51773RSF1GSM4909286HumanBreastIDC3.20e-021.99e-010.1081
51773RSF1GSM4909296HumanBreastIDC1.18e-07-1.73e-010.1524
51773RSF1GSM4909297HumanBreastIDC1.86e-132.26e-010.1517
51773RSF1GSM4909298HumanBreastIDC5.77e-1071.27e+000.1551
51773RSF1GSM4909311HumanBreastIDC8.64e-25-1.52e-010.1534
51773RSF1GSM4909312HumanBreastIDC4.79e-064.87e-020.1552
51773RSF1GSM4909317HumanBreastIDC1.99e-083.56e-010.1355
51773RSF1GSM4909319HumanBreastIDC6.59e-28-2.15e-010.1563
51773RSF1GSM4909320HumanBreastIDC2.45e-03-2.34e-010.1575
51773RSF1GSM4909321HumanBreastIDC2.45e-13-2.11e-010.1559
51773RSF1M5HumanBreastIDC4.71e-086.51e-010.1598
51773RSF1NCCBC14HumanBreastDCIS9.14e-034.88e-020.2021
51773RSF1NCCBC2HumanBreastDCIS1.52e-02-4.54e-020.1554
51773RSF1NCCBC5HumanBreastDCIS2.48e-03-1.08e-010.2046
51773RSF1P1HumanBreastIDC2.74e-13-4.87e-020.1527
51773RSF1P2HumanBreastIDC7.27e-038.58e-020.21
51773RSF1P3HumanBreastIDC4.20e-169.07e-010.1542
51773RSF1DCIS2HumanBreastDCIS2.50e-563.59e-010.0085
51773RSF1HTA11_3410_2000001011HumanColorectumAD1.18e-12-5.40e-010.0155
51773RSF1HTA11_2951_2000001011HumanColorectumAD2.06e-02-7.28e-010.0216
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
BreastThe 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.IDC: Invasive ductal carcinoma
DCIS: Ductal carcinoma in situ
Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
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
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:000037725Oral cavityEOLPRNA splicing, via transesterification reactions with bulged adenosine as nucleophile80/2218320/187234.20e-115.60e-0980
GO:000039825Oral cavityEOLPmRNA splicing, via spliceosome80/2218320/187234.20e-115.60e-0980
GO:000037525Oral cavityEOLPRNA splicing, via transesterification reactions80/2218324/187238.11e-119.53e-0980
GO:007182626Oral cavityEOLPribonucleoprotein complex subunit organization62/2218227/187231.42e-101.52e-0862
GO:001603226Oral cavityEOLPviral process94/2218415/187232.93e-102.58e-0894
GO:002261826Oral cavityEOLPribonucleoprotein complex assembly59/2218220/187238.55e-106.25e-0859
GO:002261326Oral cavityEOLPribonucleoprotein complex biogenesis96/2218463/187232.34e-089.81e-0796
GO:190331225Oral cavityEOLPnegative regulation of mRNA metabolic process31/221892/187233.14e-081.24e-0631
GO:005109824Oral cavityEOLPregulation of binding79/2218363/187234.86e-081.81e-0679
GO:001648223Oral cavityEOLPcytosolic transport44/2218168/187232.40e-077.45e-0644
GO:000632515Oral cavityEOLPchromatin organization84/2218409/187232.68e-078.16e-0684
GO:003311925Oral cavityEOLPnegative regulation of RNA splicing13/221825/187231.14e-062.78e-0513
GO:005079224Oral cavityEOLPregulation of viral process39/2218164/187231.40e-052.35e-0439
GO:004802523Oral cavityEOLPnegative regulation of mRNA splicing, via spliceosome9/221820/187232.23e-042.21e-039
GO:000024521Oral cavityEOLPspliceosomal complex assembly20/221879/187237.07e-045.78e-0320
GO:005110124Oral cavityEOLPregulation of DNA binding26/2218118/187231.21e-038.75e-0326
GO:001908022Oral cavityEOLPviral gene expression22/221894/187231.23e-038.84e-0322
GO:00063383Oral cavityEOLPchromatin remodeling46/2218255/187232.34e-031.44e-0246
GO:004852422Oral cavityEOLPpositive regulation of viral process16/221865/187233.17e-031.85e-0216
GO:005068622Oral cavityEOLPnegative regulation of mRNA processing9/221829/187234.94e-032.62e-029
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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
TNFTNFRSF1ATNF_TNFRSF1ATNFBreastADJ
TNFTNFRSF1BTNF_TNFRSF1BTNFBreastADJ
TNFSF13BTNFRSF17TNFSF13B_TNFRSF17BAFFBreastDCIS
TNFSF13BTNFRSF13BTNFSF13B_TNFRSF13BBAFFBreastDCIS
TNFSF13BTNFRSF13CTNFSF13B_TNFRSF13CBAFFBreastDCIS
TNFTNFRSF1ATNF_TNFRSF1ATNFBreastDCIS
TNFTNFRSF1BTNF_TNFRSF1BTNFBreastDCIS
TNFSF14TNFRSF14TNFSF14_TNFRSF14LIGHTBreastDCIS
TNFSF12TNFRSF12ATNFSF12_TNFRSF12ATWEAKBreastDCIS
TNFTNFRSF1ATNF_TNFRSF1ATNFBreastHealthy
TNFTNFRSF1BTNF_TNFRSF1BTNFBreastHealthy
TNFSF12TNFRSF12ATNFSF12_TNFRSF12ATWEAKBreastHealthy
TNFSF13BTNFRSF17TNFSF13B_TNFRSF17BAFFBreastHealthy
TNFSF13BTNFRSF13CTNFSF13B_TNFRSF13CBAFFBreastHealthy
TNFSF13BTNFRSF17TNFSF13B_TNFRSF17BAFFBreastIDC
TNFSF13BTNFRSF13CTNFSF13B_TNFRSF13CBAFFBreastIDC
TNFSF12TNFRSF12ATNFSF12_TNFRSF12ATWEAKCervixADJ
LTATNFRSF1ALTA_TNFRSF1ALTCervixADJ
LTATNFRSF1BLTA_TNFRSF1BLTCervixADJ
LTATNFRSF14LTA_TNFRSF14LTCervixADJ
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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
RSF1SNVMissense_Mutationc.1989A>Cp.Lys663Asnp.K663NQ96T23protein_codingtolerated_low_confidence(0.23)benign(0)TCGA-A2-A0EV-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
RSF1SNVMissense_Mutationnovelc.1274G>Cp.Cys425Serp.C425SQ96T23protein_codingtolerated_low_confidence(0.33)benign(0.031)TCGA-A2-A3XT-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycyclophosphamidePR
RSF1SNVMissense_Mutationrs779258393c.3217G>Ap.Glu1073Lysp.E1073KQ96T23protein_codingdeleterious(0.01)probably_damaging(0.996)TCGA-A8-A09E-01Breastbreast invasive carcinomaFemale>=65III/IVHormone TherapyanastrozoleSD
RSF1SNVMissense_Mutationnovelc.334N>Ap.Leu112Ilep.L112IQ96T23protein_codingtolerated(0.06)benign(0.321)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
RSF1SNVMissense_Mutationnovelc.3529G>Cp.Glu1177Glnp.E1177QQ96T23protein_codingdeleterious(0.02)possibly_damaging(0.725)TCGA-AN-A0FL-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
RSF1SNVMissense_Mutationc.2074G>Cp.Glu692Glnp.E692QQ96T23protein_codingdeleterious(0.03)benign(0.203)TCGA-AN-A0XW-01Breastbreast invasive carcinomaFemale<65III/IVUnknownUnknownSD
RSF1SNVMissense_Mutationc.1645N>Tp.Asp549Tyrp.D549YQ96T23protein_codingdeleterious_low_confidence(0)benign(0.406)TCGA-BH-A0DG-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapytaxotereCR
RSF1SNVMissense_Mutationc.2905N>Cp.Glu969Glnp.E969QQ96T23protein_codingdeleterious(0.04)possibly_damaging(0.734)TCGA-D8-A27G-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
RSF1SNVMissense_Mutationnovelc.3947N>Cp.Gly1316Alap.G1316AQ96T23protein_codingtolerated_low_confidence(0.19)benign(0.15)TCGA-LL-A5YL-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamycinSD
RSF1insertionIn_Frame_Insnovelc.1529_1530insCCTp.Arg510delinsSerLeup.R510delinsSLQ96T23protein_codingTCGA-BH-A0AY-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapySD
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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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