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Linked cancer genome atlas database

Muhammad Saleem, Shanmukha S. Padmanabhuni, Axel-Cyrille Ngonga Ngomo, Jonas S. Almeida, Stefan Decker, Helena F. Deus
2013 Proceedings of the 9th International Conference on Semantic Systems - I-SEMANTICS '13  
The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional pilot project to create an atlas of genetic mutations responsible for cancer.  ...  One of the aims of this project is to develop an infrastructure for making the cancer  ...  INTRODUCTION The Cancer Genome Atlas (TCGA) 2 is an effort led by the National Cancer Institute 3 and aims to characterize and sequence 33 cancer types from 9000 patients at the molecular level.  ... 
doi:10.1145/2506182.2506200 dblp:conf/i-semantics/SaleemPNADD13 fatcat:yqnirifszfaidehozzjdhoy6b4

Atlas of Genetics and Cytogenetics in Oncology and Haematology in 2013

Jean-Loup Huret, Mohammad Ahmad, Mélanie Arsaban, Alain Bernheim, Jérémy Cigna, François Desangles, Jean-Christophe Guignard, Marie-Christine Jacquemot-Perbal, Maureen Labarussias, Vanessa Leberre, Anne Malo, Catherine Morel-Pair (+7 others)
2012 Nucleic Acids Research  
The Atlas of Genetics and Cytogenetics in Oncology and Haematology (http://AtlasGeneticsOncology. org) is a peer-reviewed internet journal/encyclopaedia/database focused on genes implicated in cancer,  ...  As the Atlas combines different types of information (genes, genetic abnormalities, histopathology, clinical diagnoses and external links), its content is currently unique.  ...  A portal with numerous links devoted to genetics and/or cancer adds to the information available in the Atlas.  ... 
doi:10.1093/nar/gks1082 pmid:23161685 pmcid:PMC3531131 fatcat:7eacypwxrrdlbixi7qboyfax4q

Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003

J.-L. Huret
2003 Nucleic Acids Research  
This database is made for and by researchers and clinicians, who are encouraged to contribute. The Atlas is part of the genome project and it participates in research on cancer epidemiology.  ...  The 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' (http://www.infobiogen.fr/services/ chromcancer) contains concise and updated cards on genes involved in cancer, cytogenetics and clinical  ...  ACKNOWLEDGEMENTS The Atlas is funded by: Ministère de la Recherche, Ministère de l'Education Nationale, Département de la Vienne, Communauté d' Agglomération de Poitiers, Ligue Nationale contre le Cancer  ... 
doi:10.1093/nar/gkg126 pmid:12520000 pmcid:PMC165573 fatcat:i7xywqanw5blbemp3znf3eclxm

Eukaryotic Molecular Biology Databases: An Overview

Kumar Girish
2018 Highlights in BioScience  
Here we brefly described some recently published molecular databases.  ...  A straightforward database could be a single folder comprising several data, each carrying the same number of data.  ...  More than 385,000 released PTM locations with 3.6 million replacements from the Cancer Genome Atlas (TCGA), the ClinVar disease gene database, and human genome mapping projects were incorporated (8) .  ... 
doi:10.36462/h.biosci.20184 fatcat:dmii2ivldff5pbcxvkv2mkr2aa

General resources in Genetics and/or Oncology

Etienne De Braekeleer, Jean Loup Huret, Hossain Mossafa, Katriina Hautaviita, Philippe Dessen
2017 Atlas of Genetics and Cytogenetics in Oncology and Haematology  
This "Deep Insight" is a detailed subchapter of a general review article and summary on Internet databases for cytogeneticists: Internet databases and resources for cytogenetics and cytogenomics.  ...  The GDC supports several cancer genome programs at the NCI Center for Cancer Genomics (CCG), including The Cancer Genome Atlas (TCGA), Therapeutically Applicable Research to Generate Effective Treatments  ...  A pilot project, initiated in 2006, focused on analysing three types of human cancers: Glioblastoma multiforme, lung cancer, and Ovarian cancer (Cancer Genome Atlas Research Network, 2011).  ... 
doi:10.4267/2042/62946 fatcat:ogpkbnstcnbrnm6pawmf32npua

General resources in Genetics and/or Oncology

Etienne De Braekeleer, Jean Loup Huret, Hossain Mossafa, Katriina Hautaviita, Philippe Dessen
2017 Atlas of Genetics and Cytogenetics in Oncology and Haematology  
This "Deep Insight" is a detailed subchapter of a general review article and summary on Internet databases for cytogeneticists: Internet databases and resources for cytogenetics and cytogenomics.  ...  The GDC supports several cancer genome programs at the NCI Center for Cancer Genomics (CCG), including The Cancer Genome Atlas (TCGA), Therapeutically Applicable Research to Generate Effective Treatments  ...  A pilot project, initiated in 2006, focused on analysing three types of human cancers: Glioblastoma multiforme, lung cancer, and Ovarian cancer (Cancer Genome Atlas Research Network, 2011).  ... 
doi:10.4267/2042/62779 fatcat:j3jbmjapd5b3ndhz2xsf7mgaki

A database on cytogenetics in haematology and oncology

F. Dorkeld, A. Bernheim, P. Dessen, J.-L. Huret
1999 Nucleic Acids Research  
The aim of 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' (http://www.infobiogen. fr/services/chromcancer ) is to present summarized information on chromosome abnormalities in cancer,  ...  with extensions to genes involved in cancer and to cancer-prone diseases.  ...  It will be a link to other databases such as the probe resources and other various actors of the genome program.  ... 
doi:10.1093/nar/27.1.353 pmid:9847226 pmcid:PMC148181 fatcat:f3k3vrpi4ve7nabu2bhf3uu5im

Identifying Scientific Project-generated Data Citation from Full-text Articles: An Investigation of TCGA Data Citation

Jiao Li, Si Zheng, Hongyu Kang, Zhen Hou & Qing Qian
2016 Journal of Data and Information Science  
Here, we investigated the data usage of a government-funded cancer genomics project, The Cancer Genome Atlas (TCGA), via a full-text literature analysis.  ...  Purpose: In the open science era, it is typical to share project-generated scientific data by depositing it in an open and accessible database.  ...  We extracted a set of full-text articles from PMC using the query "TCGA" or "Cancer Genome Atlas" and using the publication date of 2008 (Search term: (tcga OR "cancer genome atlas") AND ("2008" [Publication  ... 
doi:10.20309/jdis.201612 fatcat:xf5huk4cbvdd5h55lpjbupyjla

Identifying Scientific Project-generated Data Citation from Full-text Articles: An Investigation of TCGA Data Citation

Jiao Li, Jiao Li, Si Zheng, Hongyu Kang, Zhen Hou & Qing Qian, Si Zheng, Hongyu Kang, Zhen Hou & Qing Qian
2016 Journal of Data and Information Science  
Here, we investigated the data usage of a government-funded cancer genomics project, The Cancer Genome Atlas (TCGA), via a full-text literature analysis.  ...  Purpose: In the open science era, it is typical to share project-generated scientific data by depositing it in an open and accessible database.  ...  We extracted a set of full-text articles from PMC using the query "TCGA" or "Cancer Genome Atlas" and using the publication date of 2008 (Search term: (tcga OR "cancer genome atlas") AND ("2008" [Publication  ... 
doi:10.20309/jdis.201600 fatcat:g45prlnbj5dw3meeb5mqc7hxbq

Application of open-access databases to determine functional connectivity between resveratrol-binding protein QR2 and colorectal carcinoma

Barbara B. Doonan, Evelien Schaafsma, John T. Pinto, Joseph M. Wu, Tze-chen Hsieh
2017 In vitro Cellular & Developmental Biology-Animal  
Two resveratrol associated genes, adenomatous polyposis coli (APC) and TP53 found in CRC were further mined, using cBio portal and Colorectal Cancer Atlas which predicted a mechanistic link to exist between  ...  This approach resembles a BioGPS, a capability for mining Web-based databases that can elucidate the potential links between compounds to provide correlations of these interactions with specific diseases  ...  The cBio Cancer Genomics Portal (http://cbioportal.org) is a resource for exploring, visualizing, and analyzing data from multidimensional cancer genomics by reducing molecular profiles from cancer tissues  ... 
doi:10.1007/s11626-017-0174-x pmid:28646291 fatcat:qbqiul3wk5e4fknqcj3vo5mm5e

Biological Databases for Human Research

Dong Zou, Lina Ma, Jun Yu, Zhang Zhang
2015 Genomics, Proteomics & Bioinformatics  
The completion of the Human Genome Project lays a foundation for systematically studying the human genome from evolutionary history to precision medicine against diseases.  ...  With the explosive growth of biological data, there is an increasing number of biological databases that have been developed in aid of human-related research.  ...  Toward this end, there are two well-known cancer projects, viz., The Cancer Genome Atlas (TCGA) [32] and International Cancer Genome Consortium (ICGC) [33] .  ... 
doi:10.1016/j.gpb.2015.01.006 pmid:25712261 pmcid:PMC4411498 fatcat:dubusegmv5gi5gcjxfrcaqhmvy

Characterization of diagnostic and prognostic significance of cell cycle-linked genes in hepatocellular carcinoma

Jukun Wang, Yu Li, Chao Zhang, Xin Chen, Linzhong Zhu, Tao Luo
2021 Translational Cancer Research  
The transcriptome along with clinicopathological data abstracted from The Cancer Genome Atlas (TCGA) were used as a training cohort.  ...  The data of samples obtained from the International Cancer Genome Consortium (ICGC) data resource were applied in the verification of the model.  ...  TCGA, The Cancer Genome Atlas.  ... 
doi:10.21037/tcr-21-1145 pmid:35116320 pmcid:PMC8799204 fatcat:vlicglezvrgrlhjbeyzxudlxea

Genomic Common Data Model for Seamless Interoperation of Biomedical Data in Clinical Practice: Retrospective Study (Preprint)

Seo Jeong Shin, Seng Chan You, Jin Roh, Jang-Hee Kim, Seokjin Haam, Christian G. Reich, Clair Blacketer, Dae-Soon Son, Seungbin Oh, Yu Rang Park, Rae Woong Park
2018 Journal of Medical Internet Research  
Waterfall plot describing the variant profile of the top 10 genes in (a) Ajou University School of Medicine and (b) The Cancer Genome Atlas databases.  ...  According to our inclusion and exclusion criteria (Multimedia Appendix 1), we selected datasets from The Cancer Genome Atlas (TCGA), Catalogue of Somatic Mutations in Cancer, and International Cancer Genome  ...  Genome Atlas (TCGA).  ... 
doi:10.2196/13249 pmid:30912749 pmcid:PMC6454347 fatcat:75jz7rfiy5b4beasdvc7g2bdoy

Atlas of Genetics and Cytogenetics in Oncology and Haematology, an Interactive Database

J.-L. Huret
2000 Nucleic Acids Research  
The 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' (http://www.infobiogen.fr/services/ chromcancer ) is a database devoted to chromosome abnormalities in cancer, cancer-prone diseases  ...  and genes involved in cancer.  ...  The Atlas is a link to other databases such as the probe resources and the other various actors of the genome program.  ... 
doi:10.1093/nar/28.1.349 pmid:10592271 pmcid:PMC102493 fatcat:vwaztgmmqrfohe5v4wbeflr5pe

Identification of MicroRNA-Related Tumorigenesis Variants and Genes in the Cancer Genome Atlas (TCGA) Data

Chang Li, Brian Wu, Han Han, Jeff Zhao, Yongsheng Bai, Xiaoming Liu
2020 Genes  
This study provides a novel way of utilizing TCGA data and integrating multiple publicly available databases to explore cancer genomics.  ...  Anti-correlated miRNA–mRNA pairs between normal and tumor tissues obtained from The Cancer Genome Atlas (TCGA) can reveal important information behind these SNVs on MTS and their associated oncogenesis  ...  The Cancer Genome Atlas (TCGA) project provides us with a great opportunity to tackle this problem.  ... 
doi:10.3390/genes11090953 pmid:32824926 fatcat:wowfqk6shngepn5ix5oka67qne
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