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: RPS4Y1

Gene summary for RPS4Y1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

RPS4Y1

Gene ID

6192

Gene nameribosomal protein S4 Y-linked 1
Gene AliasRPS4Y
CytomapYp11.2
Gene Typeprotein-coding
GO ID

GO:0006412

UniProtAcc

P22090


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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
6192RPS4Y1GSM4909319HumanBreastIDC7.71e-115.60e-010.1563
6192RPS4Y1GSM4909320HumanBreastIDC2.92e-125.91e-010.1575
6192RPS4Y1GSM4909321HumanBreastIDC7.23e-348.04e-010.1559
6192RPS4Y1HTA11_347_2000001011HumanColorectumAD1.72e-10-3.07e-01-0.1954
6192RPS4Y1HTA11_3361_2000001011HumanColorectumAD8.65e-055.46e-01-0.1207
6192RPS4Y1HTA11_83_2000001011HumanColorectumSER9.99e-035.45e-01-0.1526
6192RPS4Y1HTA11_696_2000001011HumanColorectumAD3.79e-166.64e-01-0.1464
6192RPS4Y1HTA11_866_2000001011HumanColorectumAD9.42e-044.11e-01-0.1001
6192RPS4Y1HTA11_1391_2000001011HumanColorectumAD5.54e-149.07e-01-0.059
6192RPS4Y1HTA11_2992_2000001011HumanColorectumSER1.03e-037.22e-01-0.1706
6192RPS4Y1HTA11_7862_2000001011HumanColorectumAD1.10e-056.39e-01-0.0179
6192RPS4Y1HTA11_866_3004761011HumanColorectumAD2.39e-541.41e+000.096
6192RPS4Y1HTA11_4255_2000001011HumanColorectumSER1.05e-111.31e+000.0446
6192RPS4Y1HTA11_7663_2000001011HumanColorectumSER2.26e-121.05e+000.0131
6192RPS4Y1HTA11_10623_2000001011HumanColorectumAD1.08e-056.48e-01-0.0177
6192RPS4Y1HTA11_6801_2000001011HumanColorectumSER2.28e-121.28e+000.0171
6192RPS4Y1HTA11_10711_2000001011HumanColorectumAD2.34e-04-3.07e-010.0338
6192RPS4Y1HTA11_7696_3000711011HumanColorectumAD5.77e-218.51e-010.0674
6192RPS4Y1HTA11_6818_2000001021HumanColorectumAD5.29e-231.31e+000.0588
6192RPS4Y1HTA11_99999970781_79442HumanColorectumMSS1.57e-331.17e+000.294
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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
GCThe 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.CAG: Chronic atrophic gastritis
CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
CSG: Chronic superficial gastritis
GC: Gastric cancer
SIM: Severe intestinal metaplasia
WIM: Wild intestinal metaplasia
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
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa0517124BreastIDCCoronavirus disease - COVID-1986/867232/84651.50e-289.72e-277.27e-2786
hsa0517134BreastIDCCoronavirus disease - COVID-1986/867232/84651.50e-289.72e-277.27e-2786
hsa05171ColorectumADCoronavirus disease - COVID-19113/2092232/84659.90e-162.55e-141.63e-14113
hsa051711ColorectumADCoronavirus disease - COVID-19113/2092232/84659.90e-162.55e-141.63e-14113
hsa030102ColorectumSERRibosome92/1580167/84652.21e-263.66e-242.66e-2492
hsa051712ColorectumSERCoronavirus disease - COVID-1998/1580232/84653.33e-178.50e-166.17e-1698
hsa030103ColorectumSERRibosome92/1580167/84652.21e-263.66e-242.66e-2492
hsa051713ColorectumSERCoronavirus disease - COVID-1998/1580232/84653.33e-178.50e-166.17e-1698
hsa030104ColorectumMSSRibosome96/1875167/84651.82e-232.03e-211.24e-2196
hsa051714ColorectumMSSCoronavirus disease - COVID-19108/1875232/84656.50e-171.67e-151.03e-15108
hsa030105ColorectumMSSRibosome96/1875167/84651.82e-232.03e-211.24e-2196
hsa051715ColorectumMSSCoronavirus disease - COVID-19108/1875232/84656.50e-171.67e-151.03e-15108
hsa030106ColorectumMSI-HRibosome87/797167/84655.55e-461.80e-431.51e-4387
hsa051716ColorectumMSI-HCoronavirus disease - COVID-1991/797232/84652.21e-353.58e-333.00e-3391
hsa030107ColorectumMSI-HRibosome87/797167/84655.55e-461.80e-431.51e-4387
hsa051717ColorectumMSI-HCoronavirus disease - COVID-1991/797232/84652.21e-353.58e-333.00e-3391
hsa051718ColorectumFAPCoronavirus disease - COVID-1978/1404232/84659.94e-111.11e-086.73e-0978
hsa030108ColorectumFAPRibosome59/1404167/84652.38e-091.32e-078.05e-0859
hsa051719ColorectumFAPCoronavirus disease - COVID-1978/1404232/84659.94e-111.11e-086.73e-0978
hsa030109ColorectumFAPRibosome59/1404167/84652.38e-091.32e-078.05e-0859
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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
RPS4Y1insertionFrame_Shift_Insnovelc.443_444insCTp.Tyr149SerfsTer9p.Y149Sfs*9P22090protein_codingTCGA-CC-A7IF-01Liverliver hepatocellular carcinomaMale<65III/IVUnknownUnknownPD
RPS4Y1SNVMissense_Mutationc.230G>Tp.Arg77Leup.R77LP22090protein_codingdeleterious(0)probably_damaging(0.994)TCGA-05-4432-01Lunglung adenocarcinomaMale>=65I/IIChemotherapycisplatinCR
RPS4Y1SNVMissense_Mutationnovelc.191T>Cp.Ile64Thrp.I64TP22090protein_codingdeleterious(0.01)probably_damaging(0.981)TCGA-63-A5MS-01Lunglung squamous cell carcinomaMale>=65I/IIUnknownUnknownSD
RPS4Y1SNVMissense_Mutationrs779925430c.337C>Tp.Arg113Cysp.R113CP22090protein_codingtolerated(0.14)possibly_damaging(0.563)TCGA-CD-A4MI-01Stomachstomach adenocarcinomaMale<65III/IVUnknownUnknownPD
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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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