Introduction to TumorMutations Land Content

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Contents

TumorMutations_B37

TumorMutations Land features tumor mutation data. The data are mostly from individual research articles, which can be found from NCBI PubMed. Omicsoft does not reprocess DNA-Seq mutation data, but extracts data directly from original datasets.

Data Source

PubMed

Data Types

  • CNV data
  • Expression Array data
  • DNA-Seq Somatic Mutation data

Laboratory Methods

See individual projects.

Processing Methods

Omicsoft does not reprocess DNA-Seq mutation data, but extracts data directly from original datasets.

Expression Data: Omicsoft Affymetrix Microarray Preprocessing

Key Meta Data Columns

  • Tumor Type: The types of tumor, such as PRAD-MSKCC (prostate adenocarcinoma) and LUAD-Broad (lung adenocarcinoma)
  • Sample Type: The types of sample, indicating where the sample is from. It includes information such as whether it is from normal or tumor tissue and whether it is primary, recurrent tumor, from a cell line, etc.
  • Land Tissue: The tissue from which the cell line was derived, using OmicSoft's curation Controlled Vocabulary
  • Land Sample Type: A detailed description of the cell type from which the cell line was derived, using OmicSoft's curation Controlled Vocabulary
  • Survival days and event: When available, data is added to show overall survival (OS), as well as specific measurement of survival, such as:
    • DiseaseFreeSurvival
    • MetastatisFreeSurvival
    • ProgressionFreeSurvival
    • RecurrenceFreeSurvival

Primary Grouping

Tumor Type, some examples of which are below(>30 tumor types available):

  • PRAD-MSKCC
  • MM-Broad
  • LUAD-Broad
  • LUAD-TSP
  • PRAD-SU2C
  • EAC-Broad
  • CCA-Singapore2013
  • COAD-MSKCC
  • SKCM-Broad

Sample Distribution by Tumor Type:

SampleDistributionTumorMutation.png

Key Views

DNA Mutation

DNA-Seq Somatic Mutation Distribution:

DNAseqMutationDistributionTP53 TumorMutations.png

DNA-Seq Somatic Mutation data not only show the mutation rate of each tumor type, but also are colored by mutation types such as deletion, insertion and substitution, with subtype annotation as well.

As we can see, SCLC (Small Cell Lung Cancer) samples have the highest mutation rate. The users can further look into the Land DNA-Seq Genome Browser of individual SCLC samples:

DNAseqMutationLandscapeTP53 TumorMutationsSCLC.png

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Related Articles

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