{"id":20074742,"url":"https://github.com/greenelab/nf1_inactivation","last_synced_at":"2025-07-04T19:06:22.875Z","repository":{"id":79359673,"uuid":"64140181","full_name":"greenelab/nf1_inactivation","owner":"greenelab","description":"Using Machine Learning to Identify Glioblastoma patients with NF1 inactivation","archived":false,"fork":false,"pushed_at":"2016-12-19T13:47:27.000Z","size":80,"stargazers_count":11,"open_issues_count":1,"forks_count":5,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-04-09T04:41:43.735Z","etag":null,"topics":["analysis","cancer","gene-expression","machine-learning","methodology"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/greenelab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-07-25T14:14:04.000Z","updated_at":"2023-05-02T17:03:42.000Z","dependencies_parsed_at":"2023-03-12T07:49:44.749Z","dependency_job_id":null,"html_url":"https://github.com/greenelab/nf1_inactivation","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fnf1_inactivation","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fnf1_inactivation/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fnf1_inactivation/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fnf1_inactivation/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/greenelab","download_url":"https://codeload.github.com/greenelab/nf1_inactivation/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252580075,"owners_count":21771257,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["analysis","cancer","gene-expression","machine-learning","methodology"],"created_at":"2024-11-13T14:54:08.514Z","updated_at":"2025-05-05T21:32:13.692Z","avatar_url":"https://github.com/greenelab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# NF1 Inactivation Classifier for Glioblastoma\n\n**2016 Gregory Way, Robert Allaway,\nStephanie Bouley, Camilo Fadul,\nYolanda Sanchez, and Casey Greene**\n\n---\n\n[![DOI](https://zenodo.org/badge/18957/greenelab/nf1_inactivation.svg)](https://zenodo.org/badge/latestdoi/18957/greenelab/nf1_inactivation)\n\n## Summary\n\nThe repository contains instructions to replicate and build upon a classifier\ntrained to detect an NF1 inactivation signature in glioblastoma gene expression\ndata. We leverage publicly available data from the Cancer Genome Atlas (TCGA) to\ntrain a logistic regression classifier with an elastic net penalty using\nstochastic gradient descent.\n\nNF1 is a tumor suppressor that regulates RAS (a well characterized oncogene).\nWhen NF1 is inactivated, RAS signaling continues unabated leading to\nuncontrolled cell growth. Patients with neurofibromatosis type I (caused by\nheterozygous germline mutation of NF1) have a predisposition\nfor multiple tumor types including optic gliomas, pheochromocytomas, and\nmalignant peripheral nerve sheath tumors. Furthermore, NF1 is one of the most\ncommonly mutated genes in glioblastoma.\n\nNF1 can be inactivated genetically or by other mechanisms including microRNAs\nor targeted degradation by the proteosome\n([McGillicuddy et al. 2009](http://www.ncbi.nlm.nih.gov/pubmed/19573811)).\nTherefore, detecting inactivation solely by sequencing the NF1 gene can result\nin false negatives. Because we have previously identified compounds that are\nsynthetically lethal in NF1 inactivated cells\n([Wood et al. 2011](http://www.ncbi.nlm.nih.gov/pubmed/21697395)),\nthe ability to detect patients with NF1 inactivation signatures could inform\ntreatment decisions.\n\n## Reproducibility\n\n```bash\n# All of our results and figures can be regenerated with one command:\nbash run_pipeline.sh\n```\n\nWe provide an `environment.yml` file for python packages and use the\n[checkpoint package](https://cran.r-project.org/web/packages/checkpoint/index.html)\nfor managing R packages. We also provide a\n[Docker image](https://hub.docker.com/r/gregway/nf1_inactivation) to reproduce\nthe computing environment.\n\n## Contact\n\nPlease report all bugs and direct analysis questions by filing a\n[GitHub issue](https://github.com/greenelab/nf1_inactivation/issues)\n\nPlease direct all other correspondence to: `csgreene@mail.med.upenn.edu` or\n`yolanda.sanchez@dartmouth.edu`\n\n## Data\n\nAll data is publicly available.\n\n* TCGA data used to train the classifier was retrieved from\n[UCSC Xena](https://genome-cancer.soe.ucsc.edu/proj/site/xena/datapages/).\n* Our gene expression validation data was deposited under accession\n[GSE85033](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE85033).\n\n## Acknowledgements\n\nThis work was supported by the Genomics and Computational Biology graduate group\nat The University of Pennsylvania (G.P.W); the Gordon and Betty Moore\nFoundation’s Data-Driven Discovery Initiative (grant number GBMF 4552 to\nC.S.G.); and the American Cancer Society (grant number IRG 8200327 to C.S.G.).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fnf1_inactivation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgreenelab%2Fnf1_inactivation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fnf1_inactivation/lists"}