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: ALYREF

Gene summary for ALYREF

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

ALYREF

Gene ID

10189

Gene nameAly/REF export factor
Gene AliasALY
Cytomap17q25.3
Gene Typeprotein-coding
GO ID

GO:0000018

UniProtAcc

E9PB61


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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
10189ALYREFHTA11_2487_2000001011HumanColorectumSER5.80e-072.20e-01-0.1808
10189ALYREFHTA11_1938_2000001011HumanColorectumAD3.85e-144.77e-01-0.0811
10189ALYREFHTA11_78_2000001011HumanColorectumAD6.11e-041.33e-01-0.1088
10189ALYREFHTA11_347_2000001011HumanColorectumAD1.11e-092.32e-01-0.1954
10189ALYREFHTA11_3361_2000001011HumanColorectumAD1.09e-063.17e-01-0.1207
10189ALYREFHTA11_83_2000001011HumanColorectumSER2.04e-021.36e-01-0.1526
10189ALYREFHTA11_696_2000001011HumanColorectumAD1.74e-103.14e-01-0.1464
10189ALYREFHTA11_866_2000001011HumanColorectumAD6.14e-041.76e-01-0.1001
10189ALYREFHTA11_1391_2000001011HumanColorectumAD3.99e-164.02e-01-0.059
10189ALYREFHTA11_2992_2000001011HumanColorectumSER2.14e-073.66e-01-0.1706
10189ALYREFHTA11_7862_2000001011HumanColorectumAD2.47e-082.92e-01-0.0179
10189ALYREFHTA11_866_3004761011HumanColorectumAD1.85e-214.78e-010.096
10189ALYREFHTA11_4255_2000001011HumanColorectumSER3.40e-022.39e-010.0446
10189ALYREFHTA11_8622_2000001021HumanColorectumSER1.13e-052.34e-010.0528
10189ALYREFHTA11_10623_2000001011HumanColorectumAD2.05e-041.94e-01-0.0177
10189ALYREFHTA11_6801_2000001011HumanColorectumSER3.07e-137.02e-010.0171
10189ALYREFHTA11_10711_2000001011HumanColorectumAD1.91e-072.27e-010.0338
10189ALYREFHTA11_7696_3000711011HumanColorectumAD2.20e-163.95e-010.0674
10189ALYREFHTA11_7469_2000001011HumanColorectumAD2.51e-084.42e-01-0.0124
10189ALYREFHTA11_6818_2000001021HumanColorectumAD1.54e-062.06e-010.0588
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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:0006913ColorectumADnucleocytoplasmic transport102/3918301/187231.00e-074.85e-06102
GO:0051169ColorectumADnuclear transport102/3918301/187231.00e-074.85e-06102
GO:0044403ColorectumADbiological process involved in symbiotic interaction99/3918290/187231.02e-074.93e-0699
GO:0051052ColorectumADregulation of DNA metabolic process116/3918359/187232.47e-071.00e-05116
GO:0051701ColorectumADbiological process involved in interaction with host73/3918203/187235.08e-071.88e-0573
GO:0006403ColorectumADRNA localization71/3918201/187231.54e-064.76e-0571
GO:0051236ColorectumADestablishment of RNA localization58/3918166/187231.95e-054.01e-0458
GO:0015931ColorectumADnucleobase-containing compound transport73/3918222/187232.02e-054.10e-0473
GO:0050657ColorectumADnucleic acid transport57/3918163/187232.22e-054.39e-0457
GO:0050658ColorectumADRNA transport57/3918163/187232.22e-054.39e-0457
GO:0051168ColorectumADnuclear export53/3918154/187236.89e-051.11e-0353
GO:0001649ColorectumADosteoblast differentiation70/3918229/187233.59e-044.18e-0370
GO:0032786ColorectumADpositive regulation of DNA-templated transcription, elongation13/391827/187231.47e-031.25e-0213
GO:0051028ColorectumADmRNA transport42/3918130/187231.57e-031.32e-0242
GO:0006354ColorectumADDNA-templated transcription, elongation31/391891/187232.46e-031.90e-0231
GO:0001503ColorectumADossification106/3918408/187237.68e-034.64e-02106
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa05014ColorectumADAmyotrophic lateral sclerosis164/2092364/84654.28e-181.27e-168.09e-17164
hsa03040ColorectumADSpliceosome73/2092217/84651.73e-039.68e-036.18e-0373
hsa03015ColorectumADmRNA surveillance pathway35/209297/84657.95e-033.13e-022.00e-0235
hsa050141ColorectumADAmyotrophic lateral sclerosis164/2092364/84654.28e-181.27e-168.09e-17164
hsa030401ColorectumADSpliceosome73/2092217/84651.73e-039.68e-036.18e-0373
hsa030151ColorectumADmRNA surveillance pathway35/209297/84657.95e-033.13e-022.00e-0235
hsa050142ColorectumSERAmyotrophic lateral sclerosis138/1580364/84659.89e-192.99e-172.17e-17138
hsa050143ColorectumSERAmyotrophic lateral sclerosis138/1580364/84659.89e-192.99e-172.17e-17138
hsa050144ColorectumMSSAmyotrophic lateral sclerosis156/1875364/84651.43e-194.62e-182.83e-18156
hsa050145ColorectumMSSAmyotrophic lateral sclerosis156/1875364/84651.43e-194.62e-182.83e-18156
hsa050146ColorectumMSI-HAmyotrophic lateral sclerosis95/797364/84652.31e-211.50e-191.26e-1995
hsa050147ColorectumMSI-HAmyotrophic lateral sclerosis95/797364/84652.31e-211.50e-191.26e-1995
hsa05014210EsophagusESCCAmyotrophic lateral sclerosis266/4205364/84651.31e-202.20e-181.13e-18266
hsa0301321EsophagusESCCNucleocytoplasmic transport89/4205108/84651.20e-122.37e-111.21e-1189
hsa0301524EsophagusESCCmRNA surveillance pathway72/420597/84656.12e-074.10e-062.10e-0672
hsa0304027EsophagusESCCSpliceosome128/4205217/84653.31e-038.79e-034.50e-03128
hsa0501438EsophagusESCCAmyotrophic lateral sclerosis266/4205364/84651.31e-202.20e-181.13e-18266
hsa0301331EsophagusESCCNucleocytoplasmic transport89/4205108/84651.20e-122.37e-111.21e-1189
hsa0301534EsophagusESCCmRNA surveillance pathway72/420597/84656.12e-074.10e-062.10e-0672
hsa0304037EsophagusESCCSpliceosome128/4205217/84653.31e-038.79e-034.50e-03128
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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
ALYREFinsertionIn_Frame_Insnovelc.496_497insATGp.Asp165dupp.D165dupprotein_codingTCGA-BH-A0BZ-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapydoxorubicinCR
ALYREFSNVMissense_Mutationnovelc.626N>Cp.Arg209Thrp.R209Tprotein_codingtolerated(0.34)benign(0.028)TCGA-EA-A78R-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
ALYREFSNVMissense_Mutationc.526G>Ap.Val176Ilep.V176Iprotein_codingtolerated(0.11)possibly_damaging(0.516)TCGA-AA-3821-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownSD
ALYREFSNVMissense_Mutationnovelc.535G>Cp.Asp179Hisp.D179Hprotein_codingdeleterious(0)probably_damaging(0.994)TCGA-G4-6295-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownSD
ALYREFSNVMissense_Mutationc.712G>Ap.Gly238Serp.G238Sprotein_codingtolerated(0.12)possibly_damaging(0.576)TCGA-EI-6508-01Colorectumrectum adenocarcinomaFemale<65III/IVChemotherapyoxaliplatinSD
ALYREFSNVMissense_Mutationnovelc.353N>Tp.Ser118Phep.S118Fprotein_codingdeleterious(0)probably_damaging(0.99)TCGA-4E-A92E-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
ALYREFSNVMissense_Mutationnovelc.413N>Tp.Thr138Metp.T138Mprotein_codingdeleterious(0.02)possibly_damaging(0.82)TCGA-AJ-A3NE-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
ALYREFSNVMissense_Mutationnovelc.428N>Tp.Ala143Valp.A143Vprotein_codingdeleterious(0)possibly_damaging(0.871)TCGA-AP-A054-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVChemotherapycarboplatinPD
ALYREFSNVMissense_Mutationrs781729860c.586N>Tp.Arg196Trpp.R196Wprotein_codingdeleterious(0.05)probably_damaging(0.983)TCGA-AP-A059-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
ALYREFSNVMissense_Mutationnovelc.575N>Gp.Ile192Serp.I192Sprotein_codingdeleterious(0)benign(0.048)TCGA-AP-A1DM-01Endometriumuterine corpus endometrioid carcinomaFemale<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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