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The predictive value of BRCA1 and RAP80 mRNA expression in advanced non-small-cell lung cancer patients treated with platinum-based chemotherapy

L. Bonanno, C. Costa, M. Majem, A. Favaretto, M. Rugge, R. Rosell
2013 Annals of Oncology  
The authors stated that they had carried out a literature search of all case-control and cohort studies published as original articles in English, using PubMed.  ...  A comprehensive literature search for a systematic review should include almost all of these databases and related grey literature in different languages.  ...  The major drawback of our study lies in the use of samples obtained by a conventional biopsy.  ... 
doi:10.1093/annonc/mdt063 pmid:23429864 fatcat:vfjncovvtzfipi5j7sgkrqh4hm

The mouse Gene Expression Database (GXD): 2014 update

Constance M. Smith, Jacqueline H. Finger, Terry F. Hayamizu, Ingeborg J. McCright, Jingxia Xu, Joanne Berghout, Jeff Campbell, Lori E. Corbani, Kim L. Forthofer, Pete J. Frost, Dave Miers, David R. Shaw (+5 others)
2013 Nucleic Acids Research  
The data are acquired from the scientific literature and from researchers, including groups doing largescale expression studies.  ...  Integration with the other data in Mouse Genome Informatics (MGI) and interconnections with other databases places GXD's gene expression information in the larger biological and biomedical context.  ...  The most recently acquired large data sets include RNA in situ studies of gene expression in the day 14.5 embryo [GenePaint; (23) ]; RNA in situ and immunohistochemistry studies of gene expression in  ... 
doi:10.1093/nar/gkt954 pmid:24163257 pmcid:PMC3965015 fatcat:eogjmum57rcurgukgaz4hdqaq4

PMRD: a curated database for genes and mutants involved in plant male reproduction

Xiao Cui, Qiudao Wang, Wenzhe Yin, Huayong Xu, Zoe A Wilson, Chaochun Wei, Shenyuan Pan, Dabing Zhang
2012 BMC Plant Biology  
PMRD also provides mini tools to search and browse expression patterns of genes in microarray datasets, run BLAST searches, convert gene ID and generate gene networks.  ...  expression and phenotypic information were captured from the literature.  ...  MS genes were identified from literature and biological database searches.  ... 
doi:10.1186/1471-2229-12-215 pmid:23153247 pmcid:PMC3607949 fatcat:gdg5ee3xcjg6lhwdcz4c62ofi4

SC2disease: a manually curated database of single-cell transcriptome for human diseases

Tianyi Zhao, Shuxuan Lyu, Guilin Lu, Liran Juan, Xi Zeng, Zhongyu Wei, Jianye Hao, Jiajie Peng
2020 Nucleic Acids Research  
Furthermore, we reanalyzed gene expression matrix by unified pipeline to improve the comparability between different studies.  ...  In particular, comparing gene expression profiles between different cell types and identifying cell-type-specific genes in various diseases offers new possibilities to address biological and medical questions  ...  In addition, to to improve the comparability between different studies, we designed a unified pipeline to reanalyze the gene expression matrix of each study.  ... 
doi:10.1093/nar/gkaa838 pmid:33010177 fatcat:lhjluixppjcnzmfnpqase4ozpq

GXD: a community resource of mouse Gene Expression Data

Constance M. Smith, Jacqueline H. Finger, Terry F. Hayamizu, Ingeborg J. McCright, Jingxia Xu, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Martin Ringwald
2015 Mammalian Genome  
GXD also acquires expression data directly from researchers, including groups doing large-scale expression studies. GXD currently contains nearly 1.5 million expression results for over 13,900 genes.  ...  GXD contains information about when and where genes are expressed in different tissues in the mouse, especially during the embryonic period.  ...  In particular, we would like to thank the MGI software development team for their work to improve our web interface and its underlying infrastructure: Richard Baldarelli, Jon Beal, Olin Blodgett, Jeff  ... 
doi:10.1007/s00335-015-9563-1 pmid:25939429 pmcid:PMC4534488 fatcat:u5hoj6da5nhjlfz6jbvkhlmqxu

Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature

Kyubum Lee, Chih-Hsuan Wei, Zhiyong Lu
2020 Briefings in Bioinformatics  
There is, however, no study for summarizing and comparing existing tools for genomic variant literature mining in terms of how to search easily for information in the literature on genomic variants.  ...  Results In this article, we systematically compared currently available genomic variant recognition and normalization tools as well as the literature search engines that adopted these literature-mining  ...  AVADA [36] employs machine learning and regular expressions for improved gene-variant mapping in full-text articles. It uses 47 regular expressions to recognize genomic variants.  ... 
doi:10.1093/bib/bbaa142 pmid:32770181 pmcid:PMC8138883 fatcat:yhvvphk3obdjljwt2xj3dw2nmu

Towards the reconstruction of Brassica napus seed development FA metabolism dynamic regulatory map

Alain Tchagang, Hugo Berube, Ziying Liu, Sieu Phan, Fazel Famili, Youlian Pan
2009 2009 IEEE International Workshop on Genomic Signal Processing and Statistics  
Predictions made in this study are further validated through literature search, leading to potential new roles for LEC1, LEC2, WRI1, FUS3, MYB30, and ABI3 in controlling B. napus seed development and FA  ...  metabolism related genes, thus potential targets for genetic improvement of oil production.  ...  Interactions matrix between transcription factor and gene The TF-gene interactions matrix used in this study was inferred through a carefully selected literature search, bias towards experimental evidence  ... 
doi:10.1109/gensips.2009.5174338 dblp:conf/gensips/TchagangBLPFP09 fatcat:ojpesor4ordnrl455ljnqfn2r4

The Mnemiopsis Genome Project Portal: integrating new gene expression resources and improving data visualization

R Travis Moreland, Anh-Dao Nguyen, Joseph F Ryan, Andreas D Baxevanis
2020 Database: The Journal of Biological Databases and Curation  
With this most recent update, the Portal has significantly expanded to include in situ images, temporal developmental expression profiles and single-cell expression data.  ...  In the years following the first release of the MGP Portal, it has become evident that the inclusion of data from significant published studies on Mnemiopsis has been critical to its adoption as the centralized  ...  Acknowledgements We would like to thank Edward Cayia for searching and extracting in situ images from the published Mnemiopsis literature.  ... 
doi:10.1093/database/baaa029 pmid:32386298 fatcat:sth7gpp7rnbzbg4susseqli2ua

OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data

Hayley M. Dingerdissen, Frederic Bastian, K. Vijay-Shanker, Marc Robinson-Rechavi, Amanda Bell, Nikhita Gogate, Samir Gupta, Evan Holmes, Robel Kahsay, Jonathon Keeney, Heather Kincaid, Charles Hadley King (+3 others)
2020 JCO Clinical Cancer Informatics  
METHODS Cancer mutation, cancer differential expression, cancer expression specificity, healthy gene expression from human and mouse, literature mining for cancer mutation and cancer expression, and biomarker  ...  Sentences reporting mutation or differential expression in cancer were extracted from more than 40,000 publications, and healthy gene expression data with samples mapped to organs are available for both  ...  In the detailed search view, there are multiple evidences for ERBB2 in the literature, both for differential expression and mutation.  ... 
doi:10.1200/cci.19.00117 pmid:32142370 pmcid:PMC7101249 fatcat:qijqv25waffovfheo77vm7meey

MGDB: a comprehensive database of genes involved in melanoma

Di Zhang, Rongrong Zhu, Hanqian Zhang, Chun-Hou Zheng, Junfeng Xia
2015 Database: The Journal of Biological Databases and Curation  
In addition, manually curated literature references have also been provided to support the inclusion of the gene in MGDB and establish its association with melanoma.  ...  Each melanoma gene was annotated in seven different aspects (General Information, Expression, Methylation, Mutation, Interaction, Pathway and Drug).  ...  9788 997 Literature evidence for Human Melanoma genes Expression of protein-coding genes 420 420 Expression in 470 SKCM a samples and 80 UVM a from TCGA database Expression of Non-coding genes  ... 
doi:10.1093/database/bav097 pmid:26424083 pmcid:PMC4589692 fatcat:3lxe4ynk6ngtvmlixw6z5porcy

Ozone Stress Responsive Gene Database (OSRGD ver. 1.1): a literature curated database for crop improvement [article]

Prachi Yadav, Usha Mina
2021 bioRxiv   pre-print
Various molecular studies have been performed and a variety of genes exhibiting expression in response to ozone stress have been identified.  ...  literature.  ...  Vivek Dhar Dwivedi, Scientist at Pathfinder Research and Training Foundation (PRTF), Greater Noida, Uttar Pradesh, India for his critical suggestions in database improvement.  ... 
doi:10.1101/2021.04.04.438353 fatcat:jtwzcsdnsjhyrkwxksxanmh5pa

Web resources for C. elegans studies

Raymond Lee
2005 WormBook  
Gene Expression Pattern Summary of published gene expression data can be found at WormBase, or C. elegans AceView.  ...  BCGSC Expression Pattern BCGSC Expression Patterns <http://elegans.bcgsc.ca/perl/eprofile/browse> lists GFP expression data which can be browsed directly or searched by gene name, tissue pattern or life  ... 
doi:10.1895/wormbook.1.48.1 pmid:18050388 fatcat:mk5xqffmfzb7zcnu462a6xd3g4

Identifying gene expression patterns associated with drug-specific survival in cancer patients

Bridget Neary, Jie Zhou, Peng Qiu
2021 Scientific Reports  
In this study, we integrated cancer type, drug treatment, and survival data with RNA-seq gene expression data from The Cancer Genome Atlas to identify genes and gene sets whose expression levels in patient  ...  Identifying genes whose expression influences drug sensitivity can help address both of these needs, elucidating the molecular pathways involved in drug efficacy and providing potential ways to predict  ...  Literature search. Literature searches were conducted using a Python script with the Bio.Entrez package from Biopython.  ... 
doi:10.1038/s41598-021-84211-y pmid:33654134 pmcid:PMC7925648 fatcat:wjq5xjjzczftxh2chs752odsiu

Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase

Erik Segerdell, Virgilio G Ponferrada, Christina James-Zorn, Kevin A Burns, Joshua D Fortriede, Wasila M Dahdul, Peter D Vize, Aaron M Zorn
2013 Journal of Biomedical Semantics  
Conclusions: The expanded and improved XAO allows enhanced capture of Xenopus research data and aids mechanisms for performing complex retrieval and analysis of gene expression, phenotypes, and antibodies  ...  The XAO, now with 1313 defined anatomical and developmental stage terms, has been integrated with Xenbase expression and anatomy term searches and it enables links between various data types including  ...  Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.  ... 
doi:10.1186/2041-1480-4-31 pmid:24139024 pmcid:PMC3816597 fatcat:x54xjgsz25hwvc7imkwx2aoysi

MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates

Eiru Kim, Sohyun Hwang, Hyojin Kim, Hongseok Shim, Byunghee Kang, Sunmo Yang, Jae Ho Shim, Seung Yeon Shin, Edward M. Marcotte, Insuk Lee
2015 Nucleic Acids Research  
Functional characterization of the mouse genes, hence, has been a long-standing goal in mammalian and human genetics.  ...  Here, we present an improved mouse co-functional network, MouseNet v2 (available at http://www.inetbio.org/mousenet), which covers 17 714 genes (>88% of coding genome) with 788 080 links, along with a  ...  CONCLUSIONS In this study, we present an improved functional gene network for the laboratory mouse, MouseNet v2, and demonstrate its improved performance for the study of laboratory mouse gene functions  ... 
doi:10.1093/nar/gkv1155 pmid:26527726 pmcid:PMC4702832 fatcat:pw434vapczcmtpxst4jas6pfgm
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