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: LSM6

Gene summary for LSM6

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

LSM6

Gene ID

11157

Gene nameLSM6 homolog, U6 small nuclear RNA and mRNA degradation associated
Gene AliasYDR378C
Cytomap4q31.22
Gene Typeprotein-coding
GO ID

GO:0000375

UniProtAcc

P62312


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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
11157LSM6LZE2THumanEsophagusESCC7.52e-057.37e-010.082
11157LSM6LZE4THumanEsophagusESCC2.46e-145.62e-010.0811
11157LSM6LZE7THumanEsophagusESCC1.22e-086.31e-010.0667
11157LSM6LZE8THumanEsophagusESCC2.35e-116.26e-010.067
11157LSM6LZE20THumanEsophagusESCC1.19e-073.18e-010.0662
11157LSM6LZE24THumanEsophagusESCC4.96e-133.77e-010.0596
11157LSM6LZE21THumanEsophagusESCC2.52e-094.29e-010.0655
11157LSM6LZE6THumanEsophagusESCC9.28e-116.11e-010.0845
11157LSM6P1T-EHumanEsophagusESCC1.28e-086.57e-010.0875
11157LSM6P2T-EHumanEsophagusESCC1.45e-701.51e+000.1177
11157LSM6P4T-EHumanEsophagusESCC3.92e-451.14e+000.1323
11157LSM6P5T-EHumanEsophagusESCC1.82e-347.42e-010.1327
11157LSM6P8T-EHumanEsophagusESCC1.46e-419.84e-010.0889
11157LSM6P9T-EHumanEsophagusESCC1.93e-216.15e-010.1131
11157LSM6P10T-EHumanEsophagusESCC5.99e-316.37e-010.116
11157LSM6P11T-EHumanEsophagusESCC3.07e-199.32e-010.1426
11157LSM6P12T-EHumanEsophagusESCC7.52e-701.31e+000.1122
11157LSM6P15T-EHumanEsophagusESCC2.36e-348.65e-010.1149
11157LSM6P16T-EHumanEsophagusESCC5.90e-471.02e+000.1153
11157LSM6P17T-EHumanEsophagusESCC1.38e-157.96e-010.1278
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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
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:0022613111EsophagusESCCribonucleoprotein complex biogenesis365/8552463/187231.74e-491.11e-45365
GO:0042254111EsophagusESCCribosome biogenesis252/8552299/187233.27e-441.04e-40252
GO:0008380111EsophagusESCCRNA splicing336/8552434/187231.74e-423.67e-39336
GO:003447015EsophagusESCCncRNA processing300/8552395/187233.09e-353.26e-32300
GO:0016072110EsophagusESCCrRNA metabolic process197/8552236/187231.31e-331.18e-30197
GO:0006364110EsophagusESCCrRNA processing189/8552225/187234.88e-333.87e-30189
GO:003466012EsophagusESCCncRNA metabolic process346/8552485/187234.35e-312.51e-28346
GO:0000375111EsophagusESCCRNA splicing, via transesterification reactions248/8552324/187233.05e-301.49e-27248
GO:0000377111EsophagusESCCRNA splicing, via transesterification reactions with bulged adenosine as nucleophile244/8552320/187232.52e-291.07e-26244
GO:0000398111EsophagusESCCmRNA splicing, via spliceosome244/8552320/187232.52e-291.07e-26244
GO:0006401110EsophagusESCCRNA catabolic process204/8552278/187233.39e-215.66e-19204
GO:0034655110EsophagusESCCnucleobase-containing compound catabolic process272/8552407/187232.92e-182.90e-16272
GO:0006402110EsophagusESCCmRNA catabolic process170/8552232/187238.70e-188.00e-16170
GO:0042274111EsophagusESCCribosomal small subunit biogenesis67/855273/187236.62e-175.38e-1567
GO:004670018EsophagusESCCheterocycle catabolic process286/8552445/187231.12e-157.47e-14286
GO:004427019EsophagusESCCcellular nitrogen compound catabolic process288/8552451/187233.03e-151.79e-13288
GO:001943918EsophagusESCCaromatic compound catabolic process295/8552467/187231.09e-145.98e-13295
GO:190136118EsophagusESCCorganic cyclic compound catabolic process307/8552495/187239.99e-144.80e-12307
GO:00304904EsophagusESCCmaturation of SSU-rRNA45/855250/187235.07e-111.63e-0945
GO:00080333EsophagusESCCtRNA processing92/8552127/187237.83e-101.93e-0892
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa0301824EsophagusESCCRNA degradation62/420579/84651.18e-079.39e-074.81e-0762
hsa0304027EsophagusESCCSpliceosome128/4205217/84653.31e-038.79e-034.50e-03128
hsa0301834EsophagusESCCRNA degradation62/420579/84651.18e-079.39e-074.81e-0762
hsa0304037EsophagusESCCSpliceosome128/4205217/84653.31e-038.79e-034.50e-03128
hsa030407LiverCirrhoticSpliceosome102/2530217/84655.69e-089.47e-075.84e-07102
hsa03018LiverCirrhoticRNA degradation44/253079/84651.43e-061.65e-051.02e-0544
hsa0304012LiverCirrhoticSpliceosome102/2530217/84655.69e-089.47e-075.84e-07102
hsa030181LiverCirrhoticRNA degradation44/253079/84651.43e-061.65e-051.02e-0544
hsa030182LiverHCCRNA degradation58/402079/84652.29e-062.19e-051.22e-0558
hsa0304022LiverHCCSpliceosome122/4020217/84655.55e-031.60e-028.91e-03122
hsa030183LiverHCCRNA degradation58/402079/84652.29e-062.19e-051.22e-0558
hsa0304032LiverHCCSpliceosome122/4020217/84655.55e-031.60e-028.91e-03122
hsa030189Oral cavityOSCCRNA degradation59/370479/84652.05e-081.91e-079.70e-0859
hsa0304016Oral cavityOSCCSpliceosome123/3704217/84657.21e-052.74e-041.40e-04123
hsa0301814Oral cavityOSCCRNA degradation59/370479/84652.05e-081.91e-079.70e-0859
hsa0304017Oral cavityOSCCSpliceosome123/3704217/84657.21e-052.74e-041.40e-04123
hsa0304026Oral cavityLPSpliceosome106/2418217/84651.30e-102.40e-091.55e-09106
hsa0301823Oral cavityLPRNA degradation39/241879/84656.98e-054.38e-042.83e-0439
hsa0304036Oral cavityLPSpliceosome106/2418217/84651.30e-102.40e-091.55e-09106
hsa0301833Oral cavityLPRNA degradation39/241879/84656.98e-054.38e-042.83e-0439
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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
LSM6SNVMissense_Mutationc.231N>Cp.Lys77Asnp.K77NP62312protein_codingdeleterious(0.05)benign(0.101)TCGA-EK-A3GK-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
LSM6SNVMissense_Mutationnovelc.7N>Ap.Leu3Ilep.L3IP62312protein_codingtolerated(0.21)benign(0.006)TCGA-AA-3950-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownSD
LSM6SNVMissense_Mutationnovelc.151T>Cp.Tyr51Hisp.Y51HP62312protein_codingtolerated(0.13)possibly_damaging(0.464)TCGA-A5-A0G2-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVUnknownUnknownSD
LSM6SNVMissense_Mutationnovelc.229A>Cp.Lys77Glnp.K77QP62312protein_codingdeleterious(0.02)benign(0.101)TCGA-B5-A11E-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
LSM6SNVMissense_Mutationnovelc.23N>Ap.Pro8Hisp.P8HP62312protein_codingdeleterious(0)probably_damaging(0.967)TCGA-B5-A1MX-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIHormone TherapymegaceSD
LSM6SNVMissense_Mutationc.49G>Ap.Gly17Argp.G17RP62312protein_codingtolerated(0.09)possibly_damaging(0.573)TCGA-E6-A1LX-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
LSM6SNVMissense_Mutationc.49G>Ap.Gly17Argp.G17RP62312protein_codingtolerated(0.09)possibly_damaging(0.573)TCGA-EY-A215-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
LSM6SNVMissense_Mutationnovelc.226N>Ap.Gln76Lysp.Q76KP62312protein_codingtolerated(0.68)benign(0.021)TCGA-O2-A52Q-01Lunglung squamous cell carcinomaFemale<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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