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Team:Paris Bettencourt/Project/Bioinformatics
From 2014.igem.org
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<h6>Meta-Analysis of Odor-Related Genes </h6><br> | <h6>Meta-Analysis of Odor-Related Genes </h6><br> | ||
<p class=text1> | <p class=text1> | ||
| - | <strong style="font-size: 125%;">Introduction</strong> | + | <strong style="font-size: 125%;">Introduction</strong><br> |
| - | The National Institute of Health's (NIH) Human Microbiome Project (HMP) attempted to "characterize microbial communities found at multiple human body sites and to look for correlations between changes in the microbiome and human health." There were several studies that sprouted from the data produced by the HMP, and one such study was done by the Huttenhower lab called HUMAnN: The HMP Unified Metabolic Analysis Network, a pipeline for efficient and accurate determination of the presence or absence and abundance of microbial pathways in a community using metagenomic data. | + | The National Institute of Health's (NIH) Human Microbiome Project (HMP) attempted to "characterize microbial communities found at multiple human body sites and to look for correlations between changes in the microbiome and human health." There were several studies that sprouted from the data produced by the HMP, and one such study was done by the Huttenhower lab called HUMAnN: The HMP Unified Metabolic Analysis Network, a pipeline for efficient and accurate determination of the presence or absence and abundance of microbial pathways in a community using metagenomic data. <br><br> |
| - | The abundances for each orthologous gene family (or groups of genes that perform approximately the same biological role) was reported in the units of read hits. This particular analysis used the KEGG Orthology (KO) database. Read hits refer to a read that maps to a gene sequence within a particular KO. These hits are weighted using two ways: 1. If a read hits multiple sequences, its weight is distributed among them in proportion to the strength of each mapping and 2. hits to longer sequences are down-weighted, since longer sequences contribute more reads to a metagenome due to the random sampling process of metagenomic studies. | + | The abundances for each orthologous gene family (or groups of genes that perform approximately the same biological role) was reported in the units of read hits. This particular analysis used the KEGG Orthology (KO) database. Read hits refer to a read that maps to a gene sequence within a particular KO. These hits are weighted using two ways: 1. If a read hits multiple sequences, its weight is distributed among them in proportion to the strength of each mapping and 2. hits to longer sequences are down-weighted, since longer sequences contribute more reads to a metagenome due to the random sampling process of metagenomic studies. <br><br> |
The goal of this sub-project was to find genes related to odor from the HUMAnN analysis and see how the odor profile of various body sites varies. </p> | The goal of this sub-project was to find genes related to odor from the HUMAnN analysis and see how the odor profile of various body sites varies. </p> | ||
Revision as of 13:44, 13 October 2014
Meta-Analysis of Odor-Related Genes
Introduction
The National Institute of Health's (NIH) Human Microbiome Project (HMP) attempted to "characterize microbial communities found at multiple human body sites and to look for correlations between changes in the microbiome and human health." There were several studies that sprouted from the data produced by the HMP, and one such study was done by the Huttenhower lab called HUMAnN: The HMP Unified Metabolic Analysis Network, a pipeline for efficient and accurate determination of the presence or absence and abundance of microbial pathways in a community using metagenomic data.
The abundances for each orthologous gene family (or groups of genes that perform approximately the same biological role) was reported in the units of read hits. This particular analysis used the KEGG Orthology (KO) database. Read hits refer to a read that maps to a gene sequence within a particular KO. These hits are weighted using two ways: 1. If a read hits multiple sequences, its weight is distributed among them in proportion to the strength of each mapping and 2. hits to longer sequences are down-weighted, since longer sequences contribute more reads to a metagenome due to the random sampling process of metagenomic studies.
The goal of this sub-project was to find genes related to odor from the HUMAnN analysis and see how the odor profile of various body sites varies.
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