genes

Summary

Summary: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.

Top Publications

  1. KASS D, Kaminski N. Evolving genomic approaches to idiopathic pulmonary fibrosis: moving beyond genes. Clin Transl Sci. 2011;4:372-9 pubmed publisher
    ..goals have not been reached, but genomic technologies have dramatically enhanced our understanding of how genes and gene networks contribute to the pathogenesis of disease...
  2. Skarnes W, Rosen B, West A, Koutsourakis M, Bushell W, Iyer V, et al. A conditional knockout resource for the genome-wide study of mouse gene function. Nature. 2011;474:337-42 pubmed publisher
    ..mouse knockout programmes are producing a permanent resource of targeted mutations in all protein-coding genes. Here we report the establishment of a high-throughput gene-targeting pipeline for the generation of reporter-..
  3. Gempe T, Beye M. Function and evolution of sex determination mechanisms, genes and pathways in insects. Bioessays. 2011;33:52-60 pubmed publisher
    Animals have evolved a bewildering diversity of mechanisms to determine the two sexes. Studies of sex determination genes--their history and function--in non-model insects and Drosophila have allowed us to begin to understand the ..
  4. Woodwark C, Bateman A. The characterisation of three types of genes that overlie copy number variable regions. PLoS ONE. 2011;6:e14814 pubmed publisher
    ..We classify these as type I, II and III CNV genes respectively...
  5. Colbourne J, Pfrender M, Gilbert D, Thomas W, Tucker A, Oakley T, et al. The ecoresponsive genome of Daphnia pulex. Science. 2011;331:555-61 pubmed publisher
    ..the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters...
  6. Aguilar Ruiz J, Rodriguez Baena D, Diaz Diaz N, Nepomuceno Chamorro I. CarGene: characterisation of sets of genes based on metabolic pathways analysis. Int J Data Min Bioinform. 2011;5:558-73 pubmed
    ..We developed a Kyoto Encyclopedia of Genes and Genomes (Kegg)-based tool that provides a friendly graphical environment for analysing gene-enrichment...
  7. Santoni F. EMdeCODE: a novel algorithm capable of reading words of epigenetic code to predict enhancers and retroviral integration sites and to identify H3R2me1 as a distinctive mark of coding versus non-coding genes. Nucleic Acids Res. 2013;41:e48 pubmed publisher
    ..Indeed EMdeCODE identifies unexpected epigenetic profiles specific for coding versus non-coding RNA, pointing towards a new role for H3R2me1 in coding regions. ..
  8. Wu D, Zhang Y. Evolution and function of de novo originated genes. Mol Phylogenet Evol. 2013;67:541-5 pubmed publisher
    De novo origination has recently been appreciated to be an important mechanism contributing to the origin of genes. Evidence indicates that de novo originated genes can evolve important and even essential functions rapidly...
  9. Elgzyri T, Parikh H, Zhou Y, Dekker Nitert M, Rönn T, Segerström A, et al. First-degree relatives of type 2 diabetic patients have reduced expression of genes involved in fatty acid metabolism in skeletal muscle. J Clin Endocrinol Metab. 2012;97:E1332-7 pubmed publisher
    ..2 diabetes (FH+) have been shown to have decreased energy expenditure and decreased expression of mitochondrial genes in skeletal muscle...

More Information

Publications69

  1. Di Stefano M, Rosa A, Belcastro V, di Bernardo D, Micheletti C. Colocalization of coregulated genes: a steered molecular dynamics study of human chromosome 19. PLoS Comput Biol. 2013;9:e1003019 pubmed publisher
    ..and gene activity is vividly illustrated by the observation that transcriptional coregulation of certain genes appears to be directly influenced by their spatial proximity...
  2. Wang J, Duncan D, Shi Z, Zhang B. WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res. 2013;41:W77-83 pubmed publisher
    ..WebGestalt can be freely accessed through http://www.webgestalt.org or http://bioinfo.vanderbilt.edu/webgestalt/. ..
  3. Xu T, Huang W, Zhang X, Ye B, Zhou H, Hou S. Identification and characterization of genes related to the development of breast muscles in Pekin duck. Mol Biol Rep. 2012;39:7647-55 pubmed publisher
    ..In current study, the genes which have relationships with breast muscle development were identified by suppression subtractive hybridization...
  4. Heideman M, Wilting R, Yanover E, Velds A, de Jong J, Kerkhoven R, et al. Dosage-dependent tumor suppression by histone deacetylases 1 and 2 through regulation of c-Myc collaborating genes and p53 function. Blood. 2013;121:2038-50 pubmed publisher
    ..barrier to constrain Myc-overexpressing thymocytes from progressing into lymphomas by regulating Myc-collaborating genes. One Myc-collaborating and p53-suppressing gene, Jdp2, was derepressed in an Hdac1/2-dependent manner and critical ..
  5. Cabiati M, Raucci S, Caselli C, Guzzardi M, D Amico A, Prescimone T, et al. Tissue-specific selection of stable reference genes for real-time PCR normalization in an obese rat model. J Mol Endocrinol. 2012;48:251-60 pubmed publisher
    ..In the Zucker rat model, no specific reference genes have been identified in myocardium, kidney, and lung, the main organs involved in this syndrome...
  6. Ehret G, Caulfield M. Genes for blood pressure: an opportunity to understand hypertension. Eur Heart J. 2013;34:951-61 pubmed publisher
    ..It is our hope that the knowledge of these and further loci will lead to improved understanding of BP pathophysiology and to the identification of new targets for drug therapy. ..
  7. Chandler C, Ofria C, Dworkin I. Runaway sexual selection leads to good genes. Evolution. 2013;67:110-9 pubmed publisher
    ..sexual selection, in which preference and display reinforce one another due to genetic correlation; or by good genes benefits, in which mate choice is advantageous because extreme displays indicate a well-adapted genotype...
  8. Brown A, Yemini E, Grundy L, Jucikas T, Schafer W. A dictionary of behavioral motifs reveals clusters of genes affecting Caenorhabditis elegans locomotion. Proc Natl Acad Sci U S A. 2013;110:791-6 pubmed publisher
    ..This analysis has revealed phenotypes not previously detected by real-time observation and has allowed clustering of mutants into related groups. Behavioral motifs provide a compact and intuitive representation of behavioral phenotypes. ..
  9. Dannenfelser R, Clark N, Ma ayan A. Genes2FANs: connecting genes through functional association networks. BMC Bioinformatics. 2012;13:156 pubmed publisher
    ..interaction networks are useful for identifying connections between lists of experimentally identified genes/proteins...
  10. Chen S, Krinsky B, Long M. New genes as drivers of phenotypic evolution. Nat Rev Genet. 2013;14:645-60 pubmed publisher
    ..evolution, genomes acquire novel genetic elements as sources of functional and phenotypic diversity, including new genes that originated in recent evolution...
  11. Naito Y, Bono H. GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts. Nucleic Acids Res. 2012;40:W592-6 pubmed publisher
    GGRNA (http://GGRNA.dbcls.jp/) is a Google-like, ultrafast search engine for genes and transcripts...
  12. Gray K, Daugherty L, Gordon S, Seal R, Wright M, Bruford E. Genenames.org: the HGNC resources in 2013. Nucleic Acids Res. 2013;41:D545-52 pubmed publisher
    ..Nomenclature Committee situated at the European Bioinformatics Institute assigns unique symbols and names to human genes. Since 2011, the data within our database has expanded largely owing to an increase in naming pseudogenes and non-..
  13. Cox J, Mann M. 1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data. BMC Bioinformatics. 2012;13 Suppl 16:S12 pubmed publisher
    ..compares quantitative data from any two 'omics' types in the context of categorical annotation of the proteins or genes. Suitable genome-wide categories are membership of proteins in biochemical pathways, their annotation with gene ..
  14. Arighi C, Lu Z, Krallinger M, Cohen K, Wilbur W, Valencia A, et al. Overview of the BioCreative III Workshop. BMC Bioinformatics. 2011;12 Suppl 8:S1 pubmed publisher
    ..Thirteen teams participated in the GN task which required the assignment of EntrezGene IDs to all named genes in full text papers without any species information being provided to a system...
  15. Sun Y, Zhou W, Liu H, Irwin D, Shen Y, Zhang Y. Genome-wide scans for candidate genes involved in the aquatic adaptation of dolphins. Genome Biol Evol. 2013;5:130-9 pubmed publisher
    ..In total, 368 (3.1%) of the genes were identified as having undergone positive selection by the branch-site model...
  16. Lu Z, Kao H, Wei C, Huang M, Liu J, Kuo C, et al. The gene normalization task in BioCreative III. BMC Bioinformatics. 2011;12 Suppl 8:S2 pubmed publisher
    ..challenge in BioCreative III where participating teams were asked to return a ranked list of identifiers of the genes detected in full-text articles. For training, 32 fully and 500 partially annotated articles were prepared...
  17. Dauncey M. Recent advances in nutrition, genes and brain health. Proc Nutr Soc. 2012;71:581-91 pubmed publisher
    ..Responses to nutrition are in turn influenced by individual differences in multiple target genes. Recent advances in genomics and epigenomics are increasing understanding of mechanisms by which nutrition and ..
  18. Saremi B, Sauerwein H, Danicke S, Mielenz M. Technical note: identification of reference genes for gene expression studies in different bovine tissues focusing on different fat depots. J Dairy Sci. 2012;95:3131-8 pubmed publisher
    Selection of stable reference genes (REF) is important in real-time PCR data normalization. Bovine tissues such as the mammary gland, liver, muscle, and s.c...
  19. Boon E, Meehan C, Whidden C, Wong D, Langille M, Beiko R. Interactions in the microbiome: communities of organisms and communities of genes. FEMS Microbiol Rev. 2014;38:90-118 pubmed publisher
    ..Microorganisms can rapidly gain and lose genes, potentially decoupling community roles from taxonomic and phylogenetic groupings...
  20. Jiao X, Sherman B, Huang D, Stephens R, Baseler M, Lane H, et al. DAVID-WS: a stateful web service to facilitate gene/protein list analysis. Bioinformatics. 2012;28:1805-6 pubmed publisher
    ..online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins...
  21. Fiocchi C. Genes and 'in-vironment': how will our concepts on the pathophysiology of inflammatory bowel disease develop in the future?. Dig Dis. 2012;30 Suppl 3:2-11 pubmed publisher
    ..Current knowledge of GXG and GXE and their impact on IBD pathogenesis is the focus of this review. ..
  22. Helmrich A, Ballarino M, Tora L. Collisions between replication and transcription complexes cause common fragile site instability at the longest human genes. Mol Cell. 2011;44:966-77 pubmed publisher
    We show that the time required to transcribe human genes larger than 800 kb spans more than one complete cell cycle, while their transcription speed equals that of smaller genes...
  23. Suthar M, Brassil M, Blahnik G, McMillan A, RAMOS H, Proll S, et al. A systems biology approach reveals that tissue tropism to West Nile virus is regulated by antiviral genes and innate immune cellular processes. PLoS Pathog. 2013;9:e1003168 pubmed publisher
    ..the loss of expression of several key components within the natural killer (NK) cell signaling pathway, including genes associated with NK cell activation, inflammatory cytokine production, and NK cell receptor signaling...
  24. Frenkel Morgenstern M, Danon T, Christian T, Igarashi T, Cohen L, Hou Y, et al. Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels. Mol Syst Biol. 2012;8:572 pubmed publisher
    ..When we compared the codon usage of cell cycle-regulated genes with that of other genes, we discovered that there is a significant preference for non-optimal codons...
  25. Schmitt P, Santini A, Vergnes A, Degremont L, de Lorgeril J. Sequence polymorphism and expression variability of Crassostrea gigas immune related genes discriminate two oyster lines contrasted in term of resistance to summer mortalities. PLoS ONE. 2013;8:e75900 pubmed publisher
    ..on their immune defenses, we aimed to analyze the gene expression and sequence polymorphism of 42 immune related genes in two oyster lines selected for their "High" (H) and "Low" (L) survival to summer mortalities...
  26. Tassy O, Pourquie O. Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases. Nucleic Acids Res. 2014;42:D882-91 pubmed publisher
    The function of genes is often evolutionarily conserved, and comparing the annotation of ortholog genes in different model organisms has proved to be a powerful predictive tool to identify the function of human genes...
  27. Zhu Y, Skogerbø G, Ning Q, Wang Z, Li B, Yang S, et al. Evolutionary relationships between miRNA genes and their activity. BMC Genomics. 2012;13:718 pubmed publisher
    ..However, evolutionary questions concerning the origin of miRNA genes and their subsequent evolution remain unexplained...
  28. Wang H, Zhao Q, Nie P, Jiang M, Song J. Identification of differentially expressed genes in Oncomelania hupensis chronically infected with Schistosoma japonicum. Exp Parasitol. 2012;130:374-83 pubmed publisher
    ..It is intriguing to continue functional studies for some genes such as pancreatic trypsin inhibitor; a hypothetical protein (HS576367) related to calcium ion binding; GST; and ..
  29. Chang G, Noegel A, Mavrich T, Muller R, Tomsho L, Ward E, et al. Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium. Genome Res. 2012;22:1098-106 pubmed publisher
    ..provides an ideal system to examine the extreme to which nucleotide bias may be employed in organizing promoters, genes, and nucleosomes across a genome...
  30. Le Niculescu H, Balaraman Y, Patel S, Ayalew M, Gupta J, Kuczenski R, et al. Convergent functional genomics of anxiety disorders: translational identification of genes, biomarkers, pathways and mechanisms. Transl Psychiatry. 2011;1:e9 pubmed publisher
    ..psychiatric disorders, there are technical challenges related to the identification and validation of candidate genes and peripheral biomarkers...
  31. Zhu J, Qin Y, Liu T, Wang J, Zheng X. Prioritization of candidate disease genes by topological similarity between disease and protein diffusion profiles. BMC Bioinformatics. 2013;14 Suppl 5:S5 pubmed publisher
    ..Based on the observation that genes causing the same or similar phenotypes tend to correlate with each other in the protein-protein interaction ..
  32. Navarro F, Galante P. RCPedia: a database of retrocopied genes. Bioinformatics. 2013;29:1235-7 pubmed publisher
    ..They have routinely been classified as processed pseudo-genes with little or no biological relevance...
  33. McGraw L, Davis J, Thomas P, Young L, Thomas J. BAC-based sequencing of behaviorally-relevant genes in the prairie vole. PLoS ONE. 2012;7:e29345 pubmed publisher
    ..ochrogaster) is an important model organism for the study of social behavior, yet our ability to correlate genes and behavior in this species has been limited due to a lack of genetic and genomic resources...
  34. Vasas V, Fernando C, Santos M, Kauffman S, Szathmary E. Evolution before genes. Biol Direct. 2012;7:1; discussion 1 pubmed publisher
    ..This is the only demonstration to date of a mechanism by which pre-template accumulation of adaptation could occur. ..
  35. Howe K, Clark M, Torroja C, Torrance J, Berthelot C, Muffato M, et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature. 2013;496:498-503 pubmed publisher
    ..for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes...
  36. Hoff K, Stanke M. WebAUGUSTUS--a web service for training AUGUSTUS and predicting genes in eukaryotes. Nucleic Acids Res. 2013;41:W123-8 pubmed publisher
    The prediction of protein coding genes is an important step in the annotation of newly sequenced and assembled genomes. AUGUSTUS is one of the most accurate tools for eukaryotic gene prediction...
  37. Niu J, Dou W, Ding T, Yang L, Shen G, Wang J. Evaluation of suitable reference genes for quantitative RT-PCR during development and abiotic stress in Panonychus citri (McGregor) (Acari: Tetranychidae). Mol Biol Rep. 2012;39:5841-9 pubmed publisher
    ..However, studies have shown that some commonly used reference genes varied among different experimental treatments, thus, systematic evaluation of reference genes is critical for ..
  38. Ivanova A, Tereshina M, Ermakova G, Belousov V, Zaraisky A. Agr genes, missing in amniotes, are involved in the body appendages regeneration in frog tadpoles. Sci Rep. 2013;3:1279 pubmed publisher
    Previous studies have shown that Agr genes, which encode thioredoxin domain-containing secreted proteins, play a critical role in limb regeneration in salamanders...
  39. Voora D, Cyr D, Lucas J, Chi J, Dungan J, McCaffrey T, et al. Aspirin exposure reveals novel genes associated with platelet function and cardiovascular events. J Am Coll Cardiol. 2013;62:1267-1276 pubmed publisher
    ..A set of 60 coexpressed genes named the "aspirin response signature" (ARS) was associated with PFS in HV1 (r = -0.31, p = 0...
  40. Druet T, Pérez Pardal L, Charlier C, Gautier M. Identification of large selective sweeps associated with major genes in cattle. Anim Genet. 2013;44:758-62 pubmed publisher
    ..Some unexpectedly long regions were identified. Among those, six contained genes known to affect traits with simple genetic architecture such as coat color or horn development...
  41. Dunaif A. Polycystic ovary syndrome in 2011: Genes, aging and sleep apnea in polycystic ovary syndrome. Nat Rev Endocrinol. 2011;8:72-4 pubmed publisher
  42. Ramirez F, Lawyer G, Albrecht M. Novel search method for the discovery of functional relationships. Bioinformatics. 2012;28:269-76 pubmed publisher
    Numerous annotations are available that functionally characterize genes and proteins with regard to molecular process, cellular localization, tissue expression, protein domain composition, protein interaction, disease association and ..
  43. Wei C, Kao H. Cross-species gene normalization by species inference. BMC Bioinformatics. 2011;12 Suppl 8:S5 pubmed publisher
    ..Gene names are often ambiguous, in that they can refer to the genes of many species. Therefore, gene normalization is a difficult challenge...
  44. Speakman J. Functional analysis of seven genes linked to body mass index and adiposity by genome-wide association studies: a review. Hum Hered. 2013;75:57-79 pubmed publisher
    ..The remaining 7 SNPs are adjacent to, or within, the genes NEGR1, TMEM18, ETV5, FLJ35779, LINGO2, SH2B1 and GIPR, most of which are less well studied than FTO, particularly ..
  45. Arighi C, Roberts P, Agarwal S, Bhattacharya S, Cesareni G, Chatr aryamontri A, et al. BioCreative III interactive task: an overview. BMC Bioinformatics. 2011;12 Suppl 8:S4 pubmed publisher
    ..The task focused on gene normalization (identifying gene mentions in the article and linking these genes to standard database identifiers), gene ranking based on the overall importance of each gene mentioned in the ..
  46. Cheng F, Li W, Zhou Y, Li J, Shen J, Lee P, et al. Prediction of human genes and diseases targeted by xenobiotics using predictive toxicogenomic-derived models (PTDMs). Mol Biosyst. 2013;9:1316-25 pubmed publisher
    ..gene-disease associations (GDAs) to infer chemical hazard profiles, identify exposure data gaps and to incorporate genes and disease networks into chemical safety evaluations...
  47. Cheung W, Ouellette B, Wasserman W. Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs). BMC Bioinformatics. 2012;13:249 pubmed publisher
    ..Comparison of MeSHOPs allows entities to be related based on shared medical themes in their literature. A web interface is provided for generating and visualizing MeSHOPs. ..
  48. Guénoche A. Multiple consensus trees: a method to separate divergent genes. BMC Bioinformatics. 2013;14:46 pubmed publisher
    ..the species tree cannot be inferred from the genetic sequences of a single gene because the evolution of different genes, and thus the gene tree topologies, may vary substantially...
  49. Zhu L, Nie L, Zhu G, Xiang L, Shao J. Advances in research of fish immune-relevant genes: a comparative overview of innate and adaptive immunity in teleosts. Dev Comp Immunol. 2013;39:39-62 pubmed publisher
    ..Fish immune-relevant genes have received considerable attention due to its role in improving understanding of both fish immunology and the ..
  50. Miwa M, Thompson P, Ananiadou S. Boosting automatic event extraction from the literature using domain adaptation and coreference resolution. Bioinformatics. 2012;28:1759-65 pubmed publisher
    ..The improved version of EventMine, incorporating the CR system and DA methods, is available at: http://www.nactem.ac.uk/EventMine/. ..
  51. Mostafavi S, Morris Q. Combining many interaction networks to predict gene function and analyze gene lists. Proteomics. 2012;12:1687-96 pubmed publisher
    ..We discuss these systems in general and focus on one specific system, GeneMANIA, that has unique features and uses different algorithms from the majority of other systems. ..
  52. Wong A, Park C, Greene C, Bongo L, Guan Y, Troyanskaya O. IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res. 2012;40:W484-90 pubmed publisher
    ..princeton.edu. ..
  53. Ishida M, Moore G. The role of imprinted genes in humans. Mol Aspects Med. 2013;34:826-40 pubmed publisher
    ..Therefore, genetic and epigenetic disruptions which alter the specific dosage of imprinted genes can lead to various developmental abnormalities often associated with fetal growth and neurological behaviour...
  54. Jiang H, Tang D, Liu Y, Zhang X, Zeng Z, Xu L, et al. Prevalence and characteristics of ?-lactamase and plasmid-mediated quinolone resistance genes in Escherichia coli isolated from farmed fish in China. J Antimicrob Chemother. 2012;67:2350-3 pubmed publisher
    ..fish gut samples from fish farmed throughout Guangdong province and tested for the presence of the ?-lactamase genes and PMQR-encoding genes using PCR and DNA sequence analysis...
  55. Acevedo Rocha C, Fang G, Schmidt M, Ussery D, Danchin A. From essential to persistent genes: a functional approach to constructing synthetic life. Trends Genet. 2013;29:273-9 pubmed publisher
    ..However, 'minimal sets' of essential genes are strongly context-dependent and, in all prokaryotic genomes sequenced to date, not a single protein-coding gene ..
  56. Takeda J, Yamasaki C, Murakami K, Nagai Y, Sera M, Hara Y, et al. H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery. Nucleic Acids Res. 2013;41:D915-9 pubmed publisher
    ..Of these loci, 35 631 were identified as potential protein-coding genes, and 22 898 of these were identical to known genes...
  57. Hitzemann R, Bottomly D, Darakjian P, Walter N, Iancu O, Searles R, et al. Genes, behavior and next-generation RNA sequencing. Genes Brain Behav. 2013;12:1-12 pubmed publisher
    ..RNA-Seq embraces the complexity of the transcriptome and provides a mechanism to understand the underlying regulatory code; the potential to inform the brain-behavior relationship is substantial. ..
  58. Djebali S, Davis C, Merkel A, Dobin A, Lassmann T, Mortazavi A, et al. Landscape of transcription in human cells. Nature. 2012;489:101-8 pubmed publisher
    ..These observations, taken together, prompt a redefinition of the concept of a gene. ..
  59. Wiens J, Hutter C, Mulcahy D, Noonan B, Townsend T, Sites J, et al. Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species. Biol Lett. 2012;8:1043-6 pubmed publisher
    ..phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33 717 base pairs), using both concatenated and species-tree methods for the first time...
  60. Wei C, Harris B, Li D, Berardini T, Huala E, Kao H, et al. Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts. Database (Oxford). 2012;2012:bas041 pubmed publisher
    ..These encouraging findings warrant further investigation with a larger number of publications to be annotated. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/ ..