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

Home

Download

Statistics

Help

Contact
Center for Computational Systems Medicine
leaf

Gene summary

leaf

Malignant transformation analysis

leaf

Malignant transformation related pathway analysis

leaf

Cell-cell communication analysis

leaf

Single-cell gene regulatory network inference analysis

leaf

Somatic mutation of malignant transformation related genes

leaf

Related drugs of malignant transformation related genes

Gene: SMIM1

Gene summary for SMIM1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

SMIM1

Gene ID

388588

Gene namesmall integral membrane protein 1 (Vel blood group)
Gene AliasVel
Cytomap1p36.32
Gene Typeprotein-coding
GO ID

GO:0005575

UniProtAcc

B2RUZ4


Top

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
388588SMIM1LZE24THumanEsophagusESCC1.79e-041.06e-010.0596
388588SMIM1P2T-EHumanEsophagusESCC7.91e-071.17e-010.1177
388588SMIM1P4T-EHumanEsophagusESCC3.27e-153.23e-010.1323
388588SMIM1P8T-EHumanEsophagusESCC1.24e-061.43e-010.0889
388588SMIM1P9T-EHumanEsophagusESCC2.24e-059.14e-020.1131
388588SMIM1P11T-EHumanEsophagusESCC6.15e-051.79e-010.1426
388588SMIM1P16T-EHumanEsophagusESCC3.74e-101.48e-010.1153
388588SMIM1P21T-EHumanEsophagusESCC6.38e-091.73e-010.1617
388588SMIM1P22T-EHumanEsophagusESCC1.82e-065.32e-020.1236
388588SMIM1P23T-EHumanEsophagusESCC5.57e-031.06e-010.108
388588SMIM1P24T-EHumanEsophagusESCC2.06e-034.48e-020.1287
388588SMIM1P26T-EHumanEsophagusESCC1.00e-131.09e-010.1276
388588SMIM1P27T-EHumanEsophagusESCC1.14e-023.23e-020.1055
388588SMIM1P37T-EHumanEsophagusESCC2.03e-067.63e-020.1371
388588SMIM1P39T-EHumanEsophagusESCC4.36e-036.23e-030.0894
388588SMIM1P40T-EHumanEsophagusESCC2.88e-041.45e-010.109
388588SMIM1P42T-EHumanEsophagusESCC3.56e-041.20e-010.1175
388588SMIM1P48T-EHumanEsophagusESCC1.51e-046.64e-020.0959
388588SMIM1P49T-EHumanEsophagusESCC1.84e-068.20e-010.1768
388588SMIM1P54T-EHumanEsophagusESCC6.99e-111.53e-010.0975
Page: 1 2 3 4 

check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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
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.

Top

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).
Page: 1 2 3 4 5 6 7 8 9 

check button Enriched GO biological processes.
GO IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustCount
GO:00017017BreastPrecancerin utero embryonic development35/1080367/187232.47e-032.27e-0235
GO:000170113BreastIDCin utero embryonic development42/1434367/187235.85e-034.24e-0242
GO:000170122BreastDCISin utero embryonic development41/1390367/187235.74e-034.13e-0241
GO:0001701ColorectumADin utero embryonic development110/3918367/187232.36e-054.62e-04110
GO:00017011ColorectumSERin utero embryonic development77/2897367/187232.77e-032.48e-0277
GO:00017012ColorectumMSSin utero embryonic development99/3467367/187233.71e-057.10e-0499
GO:00017013ColorectumFAPin utero embryonic development81/2622367/187231.58e-054.10e-0481
GO:00017014ColorectumCRCin utero embryonic development57/2078367/187235.54e-034.19e-0257
GO:000170119EsophagusESCCin utero embryonic development243/8552367/187231.00e-156.86e-14243
GO:000182412EsophagusESCCblastocyst development73/8552106/187231.13e-061.40e-0573
GO:00017015LiverCirrhoticin utero embryonic development134/4634367/187232.78e-076.86e-06134
GO:000170111LiverHCCin utero embryonic development204/7958367/187232.44e-074.30e-06204
GO:00017016LungIACin utero embryonic development68/2061367/187231.12e-053.45e-0468
GO:000170112LungAISin utero embryonic development59/1849367/187231.20e-042.75e-0359
GO:000170116Oral cavityOSCCin utero embryonic development207/7305367/187237.92e-122.95e-10207
GO:00018243Oral cavityOSCCblastocyst development66/7305106/187231.04e-061.40e-0566
GO:000170117Oral cavityLPin utero embryonic development142/4623367/187231.48e-096.75e-08142
GO:000182411Oral cavityLPblastocyst development46/4623106/187231.86e-053.15e-0446
GO:000170123Oral cavityEOLPin utero embryonic development72/2218367/187231.02e-051.83e-0472
GO:000170110ProstateBPHin utero embryonic development104/3107367/187239.17e-093.10e-07104
Page: 1 2 

check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
Page: 1 

Top

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
Page: 1 

Top

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.
Page: 1 

Top

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
SMIM1deletionFrame_Shift_Delnovelc.201delCp.Tyr68ThrfsTer?p.Y68Tfs*?B2RUZ4protein_codingTCGA-EW-A2FV-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapydocetaxelSD
SMIM1SNVMissense_Mutationnovelc.106C>Tp.Arg36Cysp.R36CB2RUZ4protein_codingdeleterious(0.03)benign(0.339)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
SMIM1SNVMissense_Mutationrs758771367c.107N>Ap.Arg36Hisp.R36HB2RUZ4protein_codingtolerated(0.09)benign(0.11)TCGA-EA-A556-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
SMIM1SNVMissense_Mutationrs543695662c.166G>Ap.Gly56Serp.G56SB2RUZ4protein_codingtolerated(0.17)possibly_damaging(0.858)TCGA-EI-6507-01Colorectumrectum adenocarcinomaMale<65I/IIUnknownUnknownSD
SMIM1SNVMissense_Mutationnovelc.79T>Cp.Ser27Prop.S27PB2RUZ4protein_codingtolerated(0.29)benign(0)TCGA-FI-A2D5-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVChemotherapycarboplatinumPD
Page: 1 

Top

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
Page: 1