131 research outputs found
DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes
BACKGROUND: The comparative genomic analysis of a large number of orthologous promoter regions of the chordate and plant genes from the DoOP databases shows thousands of conserved motifs. Most of these motifs differ from any known transcription factor binding site (TFBS). To identify common conserved motifs, we need a specific tool to be able to search amongst them. Since conserved motifs from the DoOP databases are linked to genes, the result of such a search can give a list of genes that are potentially regulated by the same transcription factor(s). RESULTS: We have developed a new tool called DoOPSearch for the analysis of the conserved motifs in the promoter regions of chordate or plant genes. We used the orthologous promoters of the DoOP database to extract thousands of conserved motifs from different taxonomic groups. The advantage of this approach is that different sets of conserved motifs might be found depending on how broad the taxonomic coverage of the underlying orthologous promoter sequence collection is (consider e.g. primates vs. mammals or Brassicaceae vs. Viridiplantae). The DoOPSearch tool allows the users to search these motif collections or the promoter regions of DoOP with user supplied query sequences or any of the conserved motifs from the DoOP database. To find overrepresented gene ontologies, the gene lists obtained can be analysed further using a modified version of the GeneMerge program. CONCLUSION: We present here a comparative genomics based promoter analysis tool. Our system is based on a unique collection of conserved promoter motifs characteristic of different taxonomic groups. We offer both a command line and a web-based tool for searching in these motif collections using user specified queries. These can be either short promoter sequences or consensus sequences of known transcription factor binding sites. The GeneMerge analysis of the search results allows the user to identify statistically overrepresented Gene Ontology terms that might provide a clue on the function of the motifs and genes
Polymorphism of transglutaminase 2: unusually low frequency of genomic variants with deficient functions
Magreceptorok működésének genomszintü vizsgálata kromatin immunprecipitációval primer humán immun sejtekben = Decoding nuclear hormone receptor activity using chromatin immunoprecipitation in human primary immune cells
A kutatĂłmunka során szisztematikusan feltĂ©rkĂ©peztĂĽk az un RXR heterodimer tĂpusĂş receptorok szerepĂ©t a humán monocita eredetű dendritikus sejtek differenciálĂłdása Ă©s immunfunkciĂłi során. Ezek a receptorok a PPARg, LXR, VDR Ă©s RAR receptorok volta, melyeket kiegĂ©szĂtettĂĽnk az RXR receptorral is. A specikus utvonalak azonosĂtása mellett általános megállapĂtáskĂ©nt elmondhattuk, hogy ez a receptorcsalad olyan molekuláris szenzorkĂ©nt működik, mely kĂ©pes átprogramozni a sejt genkifejezĹ‘dĂ©sĂ©t kĂĽlsĹ‘ Ă©s belsĹ‘ lipid szintek változása során. Ă–sszefĂĽggĂ©st talaltunk az IL4 STAT6-on kerestĂĽli szignalizáciĂłja Ă©s a PPARg receptor között Ă©s legĂşjabban feltĂ©rkĂ©peztĂĽk a az RXR receptor genomi kötĹ‘helyeit ls cisztromikus kölcsönhatásait is. | During our work we have systematically mapped the so called RXR heterodimeric receptors roles in monocyte derived dendritic cells during differentiation and immune function. These receptors included PPARg, LXR, VDR and RXR and also included their heterodimeric partner RXR. Based on the data obtained one can conclude that besides the specialized pathways identified, these receptors act as molecular sensors in detecting changing extra and intracellular lipid levels. We have also identified an interaction between IL4 mediated STAT6 signaling and PPARg and most recently we have detrained the RXR cistrome and its interactions
DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants
DoOP (http://doop.abc.hu/) is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species. The annotated first exons of human and Arabidopsis thaliana genes were used as queries in BLAST searches to collect the most closely related orthologous first exon sequences from Chordata and Viridiplantae species. Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and plant sections of the Database of Orthologous Promoters. Release 1.0 of DoOP contains 21 061 chordate clusters from 284 different species and 7548 plant clusters from 269 different species. The database can be used to find and retrieve promoter sequences of a given gene from various species and it is also suitable to see the most trivial conserved sequence blocks in the orthologous upstream regions. Users can search DoOP with either sequence or text (annotation) to find promoter clusters of various genes. In addition to the sequence data, the positions of the conserved sequence blocks derived from multiple alignments, the positions of repetitive elements and the positions of transcription start sites known from the Eukaryotic Promoter Database (EPD) can be viewed graphically
PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeats
Identification of dispersed or interspersed repeats, most of which are derived from transposons, retrotransposons or retrovirus-like elements, is an important step in genome annotation. Software tools that compare genomic sequences with precompiled repeat reference libraries using sensitive similarity-based methods provide reliable means of finding the positions of fragments homologous to known repeats. However, their output is often incomplete and fragmented owing to the mutations (nucleotide substitutions, deletions or insertions) that can result in considerable divergence from the reference sequence. Merging these fragments to identify the whole region that represents an ancient copy of a mobile element is challenging, particularly if the element is large and suffered multiple deletions or insertions. Here we report PLOTREP, a tool designed to post-process results obtained by sequence similarity search and merge fragments belonging to the same copy of a repeat. The software allows rapid visual inspection of the results using a dot-plot like graphical output. The web implementation of PLOTREP is available at
DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes
Isolation and characterisation of 15 microsatellite loci from Lethrus apterus (Coleoptera: Geotrupidae)
Complex pattern of alternative splicing generates unusual diversity in the leader sequence of the chicken link protein mRNA
Introgression and isolation contributed to the development of Hungarian Mangalica pigs from a particular European ancient bloodline
Identification of Positive and Negative Regulatory Regions Controlling Expression of the Cartilage Matrix Protein Gene
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