{"ID": "doi:10.1101/083410", "lab": {"correspondence": [{"contact_email": "YW5kcmV3X3NjaHJvZWRlckBobXMuaGFydmFyZC5lZHU=", "@id": "/users/986b362f-4eb6-4a9c-8173-3ab267227777/", "display_title": "Andy Schroeder"}, {"contact_email": "YW5kcmVhX2Nvc29sb0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/e4a22298-1da4-4e59-8a65-9e661f47fb48/", "display_title": "Andrea Cosolo"}, {"contact_email": "c2FyYWhfcmVpZmZAaG1zLmhhcnZhcmQuZWR1", "@id": "/users/e2324f87-0625-4bbc-803b-d47677aebe08/", "display_title": "Sarah Reiff"}], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "status": "current", "title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}, "pi": {"error": "no view permissions"}}, "url": "http://biorxiv.org/lookup/doi/10.1101/083410", "award": {"project": "4DN", "name": "1U01CA200059-01", "status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "center_title": "DCIC - DCIC", "@type": ["Award", "Item"], "description": "DCIC: The goals of the 4D Nucleome (4DN) Data Coordination and Integration Center (DCIC) are to collect, store, curate, display, and analyze data generated in the 4DN Network. We have assembled a team of investigators with a strong track record in analysis of chromatin interaction data, image processing and three-dimensional data visualization, integrative analysis of genomic and epigenomic data, data portal development, large-scale computing, and development of secure and flexible cloud technologies. In Aim 1, we will develop efficient submission pipelines for data and metadata from 4DN data production groups. We will define data/metadata requirements and quality metrics in conjunction with the production groups and ensure that high-quality, well- annotated data become available to the wider scientific community in a timely manner. In Aim 2, we will develop a user-friendly data portal for the broad scientific community. This portal will provide an easy-to-navigate interface for accessing raw and intermediate data files, allow for programmatic access via APIs, and will incorporate novel analysis and visualization tools developed by DCIC as well as other Network members. For computing and storage scalability and cost-effectiveness, significant efforts will be devoted to development and deployment of cloud-based technology. We will conduct tutorials and workshops to facilitate the use of 4DN data and tools by external investigators. In Aim 3, we will coordinate and assist in conducting integrative analysis of the multiple data types. These efforts will examine key questions in higher-order chromatin organization using both sequence and image data, and the tools and algorithms developed here will be incorporated into the data portal for use by other investigators. These three aims will ensure that the data generated in 4DN will have maximal impact for the scientific community.", "@id": "/awards/1U01CA200059-01/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Connecting tumor genomics with therapeutics through multi-dimensional network modules", "status": "current", "authors": ["Webber JT", "Ranall MV", "Kaushik S", "Bandyopadhyay S"], "journal": "bioRxiv", "version": "1", "abstract": "Recent efforts have catalogued genomic, transcriptomic, epigenetic and proteomic changes in tumors, but connecting these data with effective therapeutics remains a challenge. In contrast, cancer cell lines can model therapeutic responses but only partially reflect tumor biology. Bridging this gap requires new methods of data integration to identify a common set of pathways and molecular events. Using MAGNETIC, a new method to integrate molecular profiling data using functional networks, we identify 219 gene modules in TCGA breast cancers that capture recurrent alterations, reveal new roles for H3K27 tri-methylation and accurately quantitate various cell types within the tumor microenvironment. We show that a significant portion of gene expression and methylation in tumors is poorly reproduced in cell lines due to differences in biology and microenvironment and MAGNETIC identifies therapeutic biomarkers that are robust to these differences. This work addresses a fundamental challenge in pharmacogenomics that can only be overcome by the joint analysis of patient and cell line data.", "categories": ["integrative analysis"], "date_created": "2022-08-10T16:08:30.189987+00:00", "published_by": "External", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-08-10T16:09:29.318560+00:00"}, "date_published": "2016-10-25", "public_release": "2022-08-10", "schema_version": "2", "project_release": "2022-08-10", "exp_sets_prod_in_pub": [{"status": "released", "@id": "/experiment-set-replicates/4DNESNN6H3KW/", "experimentset_type": "replicate", "uuid": "431106bc-8535-4448-903e-854af460b116", "accession": "4DNESNN6H3KW", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNESNN6H3KW", "experiments_in_set": [{"error": "no view permissions"}, {"error": "no view permissions"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/publications/52e85c70-fe2d-11e3-9191-0800200c9a68/", "@type": ["Publication", "Item"], "uuid": "52e85c70-fe2d-11e3-9191-0800200c9a68", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Webber JT et al. (2016) doi:10.1101/083410", "external_references": [], "short_attribution": "Webber JT et al. (2016)", "number_of_experiment_sets": 1, "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}