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MGEx-Udb: A Mammalian Uterus Database for Expression-Based Cataloguing of Genes across Conditions, Including Endometriosis and Cervical Cancer

Publication Date: May 11, 2012
Journal: PLOS ONE
Authors: Akhilesh K. Bajpai, Sravanthi Davuluri, Darshan S. Chandrashekar, Selvarajan Ilakya, et al
Volume: 7
Issue: 5
Pages: e36776
DOI: https://dx.plos.org/10.1371/journal.pone.0036776
Publisher URL: http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0036776
PubMed: http://www.ncbi.nlm.nih.gov/pubmed/22606288
PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3350469
Europe PMC: http://europepmc.org/abstract/MED/22606288
Web of Science: 000305338200042
Scopus: 84861001788
Mendeley: http://www.mendeley.com/research/mgexudb-mammalian-uterus-database-expressionbased-cataloguing-genes-across-conditions-including-endo

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{"title"=>"Mgex-Udb: A mammalian uterus database for expression-based cataloguing of genes across conditions, including endometriosis and cervical cancer", "type"=>"journal", "authors"=>[{"first_name"=>"Akhilesh K.", "last_name"=>"Bajpai", "scopus_author_id"=>"36450107100"}, {"first_name"=>"Sravanthi", "last_name"=>"Davuluri", "scopus_author_id"=>"36450281400"}, {"first_name"=>"Darshan S.", "last_name"=>"Chandrashekar", "scopus_author_id"=>"36979008900"}, {"first_name"=>"Selvarajan", "last_name"=>"Ilakya", "scopus_author_id"=>"55216541400"}, {"first_name"=>"Mahalakshmi", "last_name"=>"Dinakaran", "scopus_author_id"=>"55216636800"}, {"first_name"=>"Kshitish K.", "last_name"=>"Acharya", "scopus_author_id"=>"55851234600"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"22606288", "sgr"=>"84861001788", "doi"=>"10.1371/journal.pone.0036776", "scopus"=>"2-s2.0-84861001788", "pui"=>"364803124", "isbn"=>"1932-6203 (Electronic)\r1932-6203 (Linking)", "issn"=>"19326203"}, "id"=>"24de6861-3dc9-38b2-8606-31c64e6a5b50", "abstract"=>"BACKGROUND: Gene expression profiling of uterus tissue has been performed in various contexts, but a significant amount of the data remains underutilized as it is not covered by the existing general resources.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: We curated 2254 datasets from 325 uterus related mass scale gene expression studies on human, mouse, rat, cow and pig species. We then computationally derived a 'reliability score' for each gene's expression status (transcribed/dormant), for each possible combination of conditions and locations, based on the extent of agreement or disagreement across datasets. The data and derived information has been compiled into the Mammalian Gene Expression Uterus database (MGEx-Udb, http://resource.ibab.ac.in/MGEx-Udb/). The database can be queried with gene names/IDs, sub-tissue locations, as well as various conditions such as the cervical cancer, endometrial cycles and disorders, and experimental treatments. Accordingly, the output would be a) transcribed and dormant genes listed for the queried condition/location, or b) expression profile of the gene of interest in various uterine conditions. The results also include the reliability score for the expression status of each gene. MGEx-Udb also provides information related to Gene Ontology annotations, protein-protein interactions, transcripts, promoters, and expression status by other sequencing techniques, and facilitates various other types of analysis of the individual genes or co-expressed gene clusters.\\n\\nCONCLUSIONS/SIGNIFICANCE: In brief, MGEx-Udb enables easy cataloguing of co-expressed genes and also facilitates bio-marker discovery for various uterine conditions.", "link"=>"http://www.mendeley.com/research/mgexudb-mammalian-uterus-database-expressionbased-cataloguing-genes-across-conditions-including-endo", "reader_count"=>16, "reader_count_by_academic_status"=>{"Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>1, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>1, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Agricultural and Biological Sciences"=>9, "Medicine and Dentistry"=>3, "Social Sciences"=>3, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Social Sciences"=>{"Social Sciences"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}, "Computer Science"=>{"Computer Science"=>1}}, "reader_count_by_country"=>{"Nigeria"=>1, "India"=>3}, "group_count"=>0}

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{"files"=>["https://ndownloader.figshare.com/files/639927"], "description"=>"(with gene count) collected from various sources. In case of “PubMed & GEO” and “PubMed & ArrayExpress”, smaller gene lists came from validation experiments and were collected from PubMed, while raw/processed data were always collected from the repositories (GEO/ArrayExpress).", "links"=>[], "tags"=>["genetics and genomics", "molecular biology", "Computational biology", "oncology"], "article_id"=>310412, "categories"=>["Molecular Biology", "Biological Sciences", "Cancer", "Genetics"], "users"=>["Akhilesh K. Bajpai", "Sravanthi Davuluri", "Darshan S. Chandrashekar", "Selvarajan Ilakya", "Mahalakshmi Dinakaran", "Kshitish K. Acharya"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036776.g004", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Datasets_/310412", "title"=>"Datasets", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 05:18:56"}
{"files"=>["https://ndownloader.figshare.com/files/639518"], "description"=>"Other species include cow and pig. Among the data collected from GEO or “PubMed & GEO”, 85% of the studies were also present in ArrayExpress, even though this is not indicated in the figure.", "links"=>[], "tags"=>["mammalian"], "article_id"=>310001, "categories"=>["Molecular Biology", "Biological Sciences", "Cancer", "Genetics"], "users"=>["Akhilesh K. Bajpai", "Sravanthi Davuluri", "Darshan S. Chandrashekar", "Selvarajan Ilakya", "Mahalakshmi Dinakaran", "Kshitish K. Acharya"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036776.g001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Source_of_data_across_various_mammalian_species_in_MGEx_Udb_/310001", "title"=>"Source of data across various mammalian species in MGEx-Udb.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 05:16:42"}
{"files"=>["https://ndownloader.figshare.com/files/639655"], "description"=>"(and studies) in MGEx-Udb corresponding to various physiological and pathological uterine conditions. ‘Others’ represent post-parturition, genetic-ablation, artificial insemination and embryo implantation. Studies considering tissues that are used as controls but may not be absolutely ‘normal’ have been grouped in ‘may be normal’ category (examples: “normal tissue adjacent to tumor/cancer tissue”, “vehicle-treated”).", "links"=>[], "tags"=>["genetics and genomics", "molecular biology", "Computational biology", "oncology"], "article_id"=>310140, "categories"=>["Molecular Biology", "Biological Sciences", "Cancer", "Genetics"], "users"=>["Akhilesh K. Bajpai", "Sravanthi Davuluri", "Darshan S. Chandrashekar", "Selvarajan Ilakya", "Mahalakshmi Dinakaran", "Kshitish K. Acharya"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036776.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_datasets_/310140", "title"=>"Number of datasets", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 05:17:32"}
{"files"=>["https://ndownloader.figshare.com/files/640262"], "description"=>"The figure represents the data collection (top portion), architecture (central portion) and operation (bottom portion) of the database.", "links"=>[], "tags"=>["genetics and genomics", "molecular biology", "Computational biology", "oncology"], "article_id"=>310745, "categories"=>["Molecular Biology", "Biological Sciences", "Cancer", "Genetics"], "users"=>["Akhilesh K. Bajpai", "Sravanthi Davuluri", "Darshan S. Chandrashekar", "Selvarajan Ilakya", "Mahalakshmi Dinakaran", "Kshitish K. Acharya"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036776.g006", "stats"=>{"downloads"=>5, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_MGEx_Udb_/310745", "title"=>"Schematic representation of MGEx-Udb.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 05:20:43"}
{"files"=>["https://ndownloader.figshare.com/files/640060"], "description"=>"An example (“stage IIA non-keratinizing squamous cell cervical carcinoma”) hierarchy of the conditions and sub-conditions, for which data have been collected, and drop-down options provided in the query and upload pages of MGEx-Udb. Currently the database allows up to four levels of the hierarchy to query.", "links"=>[], "tags"=>["hierarchy", "conditions"], "article_id"=>310547, "categories"=>["Molecular Biology", "Biological Sciences", "Cancer", "Genetics"], "users"=>["Akhilesh K. Bajpai", "Sravanthi Davuluri", "Darshan S. Chandrashekar", "Selvarajan Ilakya", "Mahalakshmi Dinakaran", "Kshitish K. Acharya"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036776.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_hierarchy_of_the_conditions_and_sub_conditions_/310547", "title"=>"Example hierarchy of the conditions and sub-conditions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 05:19:39"}
{"files"=>["https://ndownloader.figshare.com/files/639802"], "description"=>"‘Others’ include datasets contributed mainly by GE Healthcare and Illumina platforms.", "links"=>[], "tags"=>["microarray", "platforms"], "article_id"=>310290, "categories"=>["Molecular Biology", "Biological Sciences", "Cancer", "Genetics"], "users"=>["Akhilesh K. Bajpai", "Sravanthi Davuluri", "Darshan S. Chandrashekar", "Selvarajan Ilakya", "Mahalakshmi Dinakaran", "Kshitish K. Acharya"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036776.g003", "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Datasets_across_various_microarray_platforms_in_MGEx_Udb_/310290", "title"=>"Datasets across various microarray platforms in MGEx-Udb.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 05:18:19"}

PMC Usage Stats 81617 Mar 15:06 UTC

PMC Usage Stats | Further Information

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Relative Metric 34966610 May 16:34 UTC

Relative Metric

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F1000Prime07 Apr 11:11 UTC

F1000Prime

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