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: RIF1

Gene summary for RIF1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

RIF1

Gene ID

55183

Gene namereplication timing regulatory factor 1
Gene AliasRIF1
Cytomap2q23.3
Gene Typeprotein-coding
GO ID

GO:0000018

UniProtAcc

Q5UIP0


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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
55183RIF1CA_HPV_1HumanCervixCC3.72e-03-4.79e-020.0264
55183RIF1CCI_1HumanCervixCC4.42e-025.65e-010.528
55183RIF1CCI_2HumanCervixCC6.25e-121.06e+000.5249
55183RIF1CCI_3HumanCervixCC1.20e-056.27e-010.516
55183RIF1HTA11_3410_2000001011HumanColorectumAD2.29e-13-4.77e-010.0155
55183RIF1HTA11_2487_2000001011HumanColorectumSER2.92e-03-3.72e-01-0.1808
55183RIF1HTA11_3361_2000001011HumanColorectumAD2.71e-02-4.06e-01-0.1207
55183RIF1HTA11_696_2000001011HumanColorectumAD3.55e-05-3.80e-01-0.1464
55183RIF1HTA11_866_2000001011HumanColorectumAD1.36e-04-3.60e-01-0.1001
55183RIF1HTA11_1391_2000001011HumanColorectumAD2.55e-02-3.04e-01-0.059
55183RIF1HTA11_5212_2000001011HumanColorectumAD1.24e-02-5.55e-01-0.2061
55183RIF1HTA11_866_3004761011HumanColorectumAD2.92e-08-4.19e-010.096
55183RIF1HTA11_10711_2000001011HumanColorectumAD1.39e-02-3.46e-010.0338
55183RIF1HTA11_7696_3000711011HumanColorectumAD9.30e-07-4.00e-010.0674
55183RIF1HTA11_6818_2000001021HumanColorectumAD2.45e-03-4.24e-010.0588
55183RIF1A001-C-207HumanColorectumFAP4.79e-02-6.15e-020.1278
55183RIF1A015-C-203HumanColorectumFAP8.66e-183.55e-02-0.1294
55183RIF1A015-C-204HumanColorectumFAP1.61e-041.60e-02-0.0228
55183RIF1A014-C-040HumanColorectumFAP2.21e-02-2.85e-03-0.1184
55183RIF1A002-C-201HumanColorectumFAP6.13e-11-1.31e-010.0324
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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
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
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:00165705CervixCChistone modification84/2311463/187231.70e-042.01e-0384
GO:20010209CervixCCregulation of response to DNA damage stimulus46/2311219/187231.92e-042.23e-0346
GO:00349685CervixCChistone lysine methylation27/2311115/187236.61e-046.09e-0327
GO:00310565CervixCCregulation of histone modification33/2311152/187237.97e-047.00e-0333
GO:00987275CervixCCmaintenance of cell number30/2311134/187237.98e-047.00e-0330
GO:00026973CervixCCregulation of immune effector process62/2311339/187239.25e-047.84e-0362
GO:00510528CervixCCregulation of DNA metabolic process65/2311359/187239.25e-047.84e-0365
GO:00026967CervixCCpositive regulation of leukocyte activation72/2311409/187231.13e-039.31e-0372
GO:00512516CervixCCpositive regulation of lymphocyte activation65/2311362/187231.15e-039.39e-0365
GO:00198274CervixCCstem cell population maintenance29/2311131/187231.17e-039.47e-0329
GO:00508676CervixCCpositive regulation of cell activation73/2311420/187231.50e-031.16e-0273
GO:00165715CervixCChistone methylation30/2311141/187231.88e-031.39e-0230
GO:19908234CervixCCresponse to leukemia inhibitory factor22/231195/187232.40e-031.70e-0222
GO:00180224CervixCCpeptidyl-lysine methylation28/2311131/187232.43e-031.71e-0228
GO:00064795CervixCCprotein methylation36/2311181/187232.46e-031.71e-0236
GO:00082135CervixCCprotein alkylation36/2311181/187232.46e-031.71e-0236
GO:00024603CervixCCadaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains62/2311356/187233.09e-032.03e-0262
GO:0002263CervixCCcell activation involved in immune response50/2311279/187234.16e-032.57e-0250
GO:19908304CervixCCcellular response to leukemia inhibitory factor21/231194/187234.68e-032.82e-0221
GO:0002443CervixCCleukocyte mediated immunity73/2311440/187235.01e-032.98e-0273
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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
RIF1SNVMissense_Mutationnovelc.2705N>Ap.Gly902Glup.G902EQ5UIP0protein_codingdeleterious(0.03)benign(0.275)TCGA-5L-AAT0-01Breastbreast invasive carcinomaFemale<65I/IIHormone TherapytamoxiphenSD
RIF1SNVMissense_Mutationc.1744N>Ap.Ala582Thrp.A582TQ5UIP0protein_codingdeleterious(0)probably_damaging(0.997)TCGA-BH-A0AZ-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapydoxorubicinCR
RIF1SNVMissense_Mutationc.4006N>Ap.Glu1336Lysp.E1336KQ5UIP0protein_codingdeleterious(0.03)benign(0.053)TCGA-BH-A0B5-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapyadriamycinCR
RIF1SNVMissense_Mutationc.4111N>Tp.Asn1371Tyrp.N1371YQ5UIP0protein_codingdeleterious(0.02)benign(0.26)TCGA-BH-A0HU-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydocetaxelSD
RIF1SNVMissense_Mutationnovelc.7033N>Tp.Pro2345Serp.P2345SQ5UIP0protein_codingdeleterious(0)probably_damaging(0.998)TCGA-C8-A8HQ-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
RIF1SNVMissense_Mutationnovelc.7196N>Cp.Leu2399Prop.L2399PQ5UIP0protein_codingdeleterious(0)possibly_damaging(0.543)TCGA-C8-A8HR-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapy5-fluorouracilCR
RIF1SNVMissense_Mutationc.7030N>Tp.Leu2344Phep.L2344FQ5UIP0protein_codingdeleterious(0)probably_damaging(0.966)TCGA-D8-A1JA-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapyadriamycinPD
RIF1SNVMissense_Mutationnovelc.6699N>Gp.Ser2233Argp.S2233RQ5UIP0protein_codingtolerated(0.12)benign(0.235)TCGA-D8-A1XK-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicine+cyclophosphamideSD
RIF1SNVMissense_Mutationc.3977N>Gp.Asn1326Serp.N1326SQ5UIP0protein_codingtolerated(0.15)possibly_damaging(0.815)TCGA-D8-A1XS-01Breastbreast invasive carcinomaMale<65III/IVChemotherapyadriamycin+cyclophosphamideSD
RIF1SNVMissense_Mutationnovelc.6515C>Tp.Ser2172Phep.S2172FQ5UIP0protein_codingdeleterious(0)probably_damaging(0.999)TCGA-E2-A152-01Breastbreast invasive carcinomaFemale<65I/IITargeted Molecular therapytrastuzumabPD
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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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