{
  "abstracts": [
    {
      "content": "Discovering all the genetic causes of a phenotype is an important goal in\nfunctional genomics. In this paper we combine an experimental design for\nmultiple independent detections of the genetic causes of a phenotype, with a\nhigh-throughput sequencing analysis that maximizes sensitivity for\ncomprehensively identifying them. Testing this approach on a set of 24 mutant\nstrains generated for a metabolic phenotype with many known genetic causes, we\nshow that this pathway-based phenotype sequencing analysis greatly improves\nsensitivity of detection compared with previous methods, and reveals a wide\nrange of pathways that can cause this phenotype. We demonstrate our approach on\na metabolic re-engineering phenotype, the PEP/OAA metabolic node in E. coli,\nwhich is crucial to a substantial number of metabolic pathways and under\nrenewed interest for biofuel research. Out of 2157 mutations in these strains,\npathway-phenoseq discriminated just five gene groups (12 genes) as\nstatistically significant causes of the phenotype. Experimentally, these five\ngene groups, and the next two high-scoring pathway-phenoseq groups, either have\na clear connection to the PEP metabolite level or offer an alternative path of\nproducing oxaloacetate (OAA), and thus clearly explain the phenotype. These\nhigh-scoring gene groups also show strong evidence of positive selection\npressure, compared with strictly neutral selection in the rest of the genome.",
      "lang": "en",
      "mimetype": "text/plain",
      "sha1": "fd1f89a43ea07ef7825734043c9d9bd56872300e"
    }
  ],
  "contribs": [
    {
      "index": 0,
      "raw_name": "Marc Harper",
      "role": "author"
    },
    {
      "index": 1,
      "raw_name": "Luisa Gronenberg",
      "role": "author"
    },
    {
      "index": 2,
      "raw_name": "James Liao",
      "role": "author"
    },
    {
      "index": 3,
      "raw_name": "Christopher Lee",
      "role": "author"
    }
  ],
  "ext_ids": {
    "arxiv": "1303.0455v1"
  },
  "extra": {
    "arxiv": {
      "base_id": "1303.0455",
      "categories": [
        "q-bio.QM",
        "q-bio.GN"
      ]
    }
  },
  "ident": "unwrwze6znf5xouud35i3jlneq",
  "language": "en",
  "license_slug": "ARXIV-1.0",
  "refs": [],
  "release_date": "2013-03-03",
  "release_stage": "submitted",
  "release_type": "article",
  "release_year": 2013,
  "revision": "d66823db-c3dd-4981-8d79-6ee5b66b358c",
  "state": "active",
  "title": "Comprehensive Detection of Genes Causing a Phenotype using Phenotype\n  Sequencing and Pathway Analysis",
  "version": "v1",
  "work_id": "a5fegh5iyrfwpc32y33envrime"
}