PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium
Reads0
Chats0
TLDR
Protein Analysis THrough Evolutionary Relationships (PANTHER) is a comprehensive software system for inferring the functions of genes based on their evolutionary relationships, resulting in an increasing number of curated functional annotations.Abstract:
Protein Analysis THrough Evolutionary Relationships (PANTHER) is a comprehensive software system for inferring the functions of genes based on their evolutionary relationships. Phylogenetic trees of gene families form the basis for PANTHER and these trees are annotated with ontology terms describing the evolution of gene function from ancestral to modern day genes. One of the main applications of PANTHER is in accurate prediction of the functions of uncharacterized genes, based on their evolutionary relationships to genes with functions known from experiment. The PANTHER website, freely available at http://www.pantherdb.org, also includes software tools for analyzing genomic data relative to known and inferred gene functions. Since 2007, there have been several new developments to PANTHER: (i) improved phylogenetic trees, explicitly representing speciation and gene duplication events, (ii) identification of gene orthologs, including least diverged orthologs (best one-to-one pairs), (iii) coverage of more genomes (48 genomes, up to 87% of genes in each genome; see http://www.pantherdb.org/panther/summaryStats.jsp), (iv) improved support for alternative database identifiers for genes, proteins and microarray probes and (v) adoption of the SBGN standard for display of biological pathways. In addition, PANTHER trees are being annotated with gene function as part of the Gene Ontology Reference Genome project, resulting in an increasing number of curated functional annotations.read more
Citations
More filters
Journal ArticleDOI
iTRAQ based characterization of proteomic change in petroleum hydrocarbon-degrading Pseudomonas aeruginosa in different pH conditions
TL;DR: Chemotaxis and uptake of carbon, terminal oxidation of short-chain alkanes and transmembrane transport which are considered as key cellular processes in biodegradation of petroleum hydrocarbons in P.aeruginosa P6 may be disturbed, while in the condition of pH 8.5, the activity of transmemBRane transport may decrease.
Patent
Methods and compositions for the treatment of amyloid diseases
TL;DR: In this paper, the authors present methods and agents for use in the treatment and prevention of diseases characterized by abnormal protein aggregation, in particular for the treatment of ATTR and Alzheimer's disease.
Bioinformatic studies of the disposition pathways and targets of synthetic drugs and herbal medicines
TL;DR: Drugs are pharmaceutical compounds administered to treat or diagnose disease and have specific reactions with molecular structures or drug targets to produce an effect.
Posted ContentDOI
HOTAIRprimes the Ewing sarcoma family of tumors for tumorigenesis via epigenetic dysregulation involving LSD1
Hasan Siddiqui,Julia Selich-Anderson,Joshua Felgenhauer,James Fitch,V Nadella,Cenny Taslim,Laura Tomino,Emily R. Theisen,Satoru Otsuru,Edwin M. Horwitz,Stephen L. Lessnick,Peter White,Nilay Shah +12 more
TL;DR: The work shows that HOTAIR is consistently expressed among ESFT and induces epigenetic and gene expression changes that cooperate in tumorigenesis and elucidate new steps of malignant transformation in this cancer and identify novel therapeutic targets.
Posted ContentDOI
Genome-wide strategies identify molecular niches regulated by connective tissue-associated transcription factors
Mickael Orgeur,Marvin Martens,Georgeta Leonte,Sonya Nassari,Marie-Ange Bonnin,Stefan T. Börno,Bernd Timmermann,Jochen Hecht,Delphine Duprez,Sigmar Stricker +9 more
TL;DR: Insight into the signalling pathways governing limb connective tissue differentiation is provided and a concept whereby local molecular niches can be created via the expression of specific transcription factors impinging on the specification of microenvironments is suggested.
References
More filters
Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Journal ArticleDOI
The Universal Protein Resource (UniProt)
Amos Marc Bairoch,Rolf Apweiler,Cathy H. Wu,Winona C. Barker,Brigitte Boeckmann,Serenella Ferro,Elisabeth Gasteiger,Hongzhan Huang,Rodrigo Lopez,Michele Magrane,Maria Jesus Martin,Darren A. Natale,Claire O'Donovan,Nicole Redaschi,Lai-Su L. Yeh +14 more
TL;DR: During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; the UniProt keyword list got augmented by additional keywords; the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications.
Journal ArticleDOI
Recent developments in the MAFFT multiple sequence alignment program
Kazutaka Katoh,Hiroyuki Toh +1 more
TL;DR: The initial version of the MAFFT program was developed in 2002 and was updated in 2007 with two new techniques: the PartTree algorithm and the Four-way consistency objective function, which improved the scalability of progressive alignment and the accuracy of ncRNA alignment.
Journal ArticleDOI
PANTHER: a library of protein families and subfamilies indexed by function.
Paul Thomas,Michael J. Campbell,Anish Kejariwal,Huaiyu Mi,Brian Karlak,Robin Daverman,Karen Diemer,Anushya Muruganujan,Apurva Narechania +8 more
TL;DR: The PANTHER/X ontology is used to give a high-level representation of gene function across the human and mouse genomes, and the family HMMs are used to rank missense single nucleotide polymorphisms (SNPs) according to their likelihood of affecting protein function.
Journal ArticleDOI
Entrez Gene: gene-centered information at NCBI
TL;DR: Entrez Gene is a step forward from NCBI's LocusLink, with both a major increase in taxonomic scope and improved access through the many tools associated with NCBI Entrez.
Related Papers (5)
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more