The Homeodomain Resource: a comprehensive collection of sequence, structure, interaction, genomic and functional information on the homeodomain protein family

The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. The current version builds upon previous versions by the addition of new, complete sets of homeodomain sequences from fully sequenced genomes, the expansion of existing curated homeodomain information and the improvement of data accessibility through better search tools and more complete data integration. This release contains 1534 full-length homeodomain-containing sequences, 93 experimentally derived homeodomain structures, 101 homeodomain protein–protein interactions, 107 homeodomain DNA-binding sites and 206 homeodomain proteins implicated in human genetic disorders. Database URL: The Homeodomain Resource is freely available and can be accessed at http://research.nhgri.nih.gov/homeodomain/

[1]  T. Saito,et al.  Structure of the rat thyroid transcription factor-1 (TTF-1) gene. , 1994, Biochemical and biophysical research communications.

[2]  Ian M. Donaldson,et al.  The Biomolecular Interaction Network Database and related tools 2005 update , 2004, Nucleic Acids Res..

[3]  E. Lewis A gene complex controlling segmentation in Drosophila , 1978, Nature.

[4]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[5]  G. Tell,et al.  Missense mutations of human homeoboxes: A review , 2001, Human mutation.

[6]  Masatoshi Nei,et al.  Evolutionary change of the numbers of homeobox genes in bilateral animals. , 2005, Molecular biology and evolution.

[7]  R. Meyers Encyclopedia of molecular cell biology and molecular medicine , 2014 .

[8]  P. Stenson,et al.  Human Gene Mutation Database (HGMD®): 2003 update , 2003, Human mutation.

[9]  W. J. Gehring,et al.  A conserved DNA sequence in homoeotic genes of the Drosophila Antennapedia and bithorax complexes , 1984, Nature.

[10]  Richard C Trembath,et al.  Missense mutations in the homeodomain of HOXD13 are associated with brachydactyly types D and E. , 2003, American journal of human genetics.

[11]  R. Kaptein,et al.  Solution structure of the POU-specific DNA-binding domain of Oct-1 , 1993, Nature.

[12]  T. Ceska,et al.  The X‐ray structure of an atypical homeodomain present in the rat liver transcription factor LFB1/HNF1 and implications for DNA binding. , 1993, The EMBO journal.

[13]  P. Stenson,et al.  Human Gene Mutation Database (HGMD , 2003 .

[14]  T. Tatusova,et al.  Entrez Gene: gene-centered information at NCBI , 2006, Nucleic Acids Res..

[15]  K. Nicholas,et al.  GeneDoc: Analysis and visualization of genetic variation , 1997 .

[16]  Cynthia Wolberger,et al.  Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. , 1991, Cell.

[17]  Raymond C Stevens,et al.  Crystal structure and DNA binding of the homeodomain of the stem cell transcription factor Nanog. , 2008, Journal of molecular biology.

[18]  Andreas D. Baxevanis,et al.  The Homeodomain Resource: sequences, structures, DNA binding sites and genomic information , 2001, Nucleic Acids Res..

[19]  J. Mullikin,et al.  The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes: evidence from the starlet sea anemone, Nematostella vectensis , 2006, Genome Biology.

[20]  W. Gehring,et al.  Homeodomain proteins. , 1994, Annual review of biochemistry.

[21]  Andreas D. Baxevanis,et al.  The Homeodomain Resource: 2003 update , 2003, Nucleic Acids Res..

[22]  Carl O. Pabo,et al.  Crystal structure of an engrailed homeodomain-DNA complex at 2.8 Å resolution: A framework for understanding homeodomain-DNA interactions , 1990, Cell.

[23]  Yanli Wang,et al.  MMDB: annotating protein sequences with Entrez's 3D-structure database , 2006, Nucleic Acids Res..

[24]  C. Kim,et al.  SHOX mutations in idiopathic short stature and Leri‐Weill dyschondrosteosis: frequency and phenotypic variability , 2006, Clinical endocrinology.

[25]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[26]  G. Gloor,et al.  Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions. , 2005, Biochemistry.

[27]  J. M. Baird-Titus,et al.  The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site. , 2006, Journal of molecular biology.

[28]  Judith A. Blake,et al.  The Mouse Genome Database (MGD): mouse biology and model systems , 2007, Nucleic Acids Res..

[29]  Tatiana Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[30]  Andreas D. Baxevanis,et al.  Searching Online Mendelian Inheritance in Man (OMIM) for Information for Genetic Loci Involved in Human Disease , 2002, Current protocols in human genetics.

[31]  David Jablonski,et al.  Morphological and developmental macroevolution: a paleontological perspective. , 2003, The International journal of developmental biology.

[32]  Daniel E. Newburger,et al.  Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences , 2008, Cell.

[33]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2002, Nucleic Acids Res..

[34]  E. Birney,et al.  The International Protein Index: An integrated database for proteomics experiments , 2004, Proteomics.

[35]  K. Shokat,et al.  A phage display selection of engrailed homeodomain mutants and the importance of residue Q50. , 2004, Nucleic acids research.

[36]  P. Holland,et al.  HomeoDB: a database of homeobox gene diversity , 2008, Evolution & development.

[37]  Y. Chi Homeodomain revisited: a lesson from disease-causing mutations , 2005, Human Genetics.

[38]  Elspeth A Bruford,et al.  Classification and nomenclature of all human homeobox genes , 2007, BMC Biology.