Interested in finding a team? The map below shows the teams in the Pacific Northwest District. Many teams are looking for new mentors. If you are a mentor who would like to get involved with a school in your area, please check out our map to find a team.Maintained by David Heiman Broad Institute TCGA Genome Data Analysis Center Mutation Analysis (MutSigCV v0.9). Broad Institute of MIT and Harvard. This report serves to describe the mutational landscape and properties of a given individual set, as well as rank genes and genesets according to mutational significance. MutSigCV v0.9 was used to generate the results found in this report. Working with individual set: COADREAD-TP Number of patients in set: 489 The input for this pipeline is a set of individuals with the following files associated for each: An annotated .maf file describing the mutations called for the respective individual, and their properties. A .wig file that contains information about the coverage of the sample.
MAF used for this analysis:COADREAD-TP.final_analysis_set.maf Blacklist used for this analysis: pancan_mutation_blacklist.v14.hg19.txt Significantly mutated genes (q ≤ 0.1): 131 The x axis represents the samples. The y axis represents the exons, one row per exon, and they are sorted by average coverage across samples. For exons with exactly the same average coverage, they are sorted next by the %GC of the exon. (The secondary sort is especially useful for the zero-coverage exons at the bottom). If the figure is unpopulated, then full coverage is assumed (e.g. MutSig CV doesn't use WIGs and assumes full coverage). The mutation spectrum is depicted in the lego plots below in which the 96 possible mutation types are subdivided into six large blocks, color-coded to reflect the base substitution type. Each large block is further subdivided into the 16 possible pairs of 5' and 3' neighbors, as listed in the 4x4 trinucleotide context legend. The height of each block corresponds to the mutation frequency for that kind of mutation (counts of mutations normalized by the base coverage in a given bin).
The shape of the spectrum is a signature for dominant mutational mechanisms in different tumor types. nnon = number of (nonsilent) mutations in this gene across the individual set npat = number of patients (individuals) with at least one nonsilent mutation nsite = number of unique sites having a non-silent mutation nflank = number of noncoding mutations from this gene's flanking region, across the individual set nsil = number of silent mutations in this gene across the individual set p = p-value (overall) q = q-value, False Discovery Rate (Benjamini-Hochberg procedure) In brief, we tabulate the number of mutations and the number of covered bases for each gene. The counts are broken down by mutation context category: four context categories that are discovered by MutSig, and one for indel and 'null' mutations, which include indels, nonsense mutations, splice-site mutations, and non-stop (read-through) mutations. For each gene, we calculate the probability of
seeing the observed constellation of mutations, i.e. the product P1 x P2 x ... x Pm, or a more extreme one, given the background mutation rates calculated across the dataset. In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal. Analysis Results (MD5 checksum) Auxiliary Data (MD5 checksum) MAGE-TAB File (MD5 checksum) Broad Institute TCGA GDAC as part of the TCGA Research Network.Store Locator & Opening Hours Postcode or town name (for stores in Northern Ireland enter a postcode) Find a store in the Republic of Ireland Welcome to the store at Argos combine the best of shopping online and shopping on the high street, offering a fast, easy and seamless way to get what you want. Browse online and check stock in your local store before reserving your item!
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