Literature DB >> 19389737

CROC: finding chromosomal clusters in eukaryotic genomes.

Miguel Pignatelli1, Florenci Serras, Andrés Moya, Roderic Guigó, Montserrat Corominas.   

Abstract

SUMMARY: There is increasing evidence showing that co-expression of genes that cluster along the genome is a common characteristic of eukaryotic transcriptomes. Several algorithms have been used to date in the identification of these kinds of gene organization. Here, we present a web tool called CROC that aims to help in the identification and analysis of genomic gene clusters. This method has been successfully used before in the identification of chromosomal clusters in different eukaryotic species. AVAILABILITY: The web server is freely available to non-commercial users at the following address: http://metagenomics.uv.es/CROC/.

Mesh:

Year:  2009        PMID: 19389737     DOI: 10.1093/bioinformatics/btp248

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  14 in total

1.  Cancer-Associated Fibroblasts in Pancreatic Cancer Are Reprogrammed by Tumor-Induced Alterations in Genomic DNA Methylation.

Authors:  Qian Xiao; Donger Zhou; Agnieszka A Rucki; Jamila Williams; Jiaojiao Zhou; Guanglan Mo; Adrian Murphy; Kenji Fujiwara; Jennifer Kleponis; Bulent Salman; Christopher L Wolfgang; Robert A Anders; Shu Zheng; Elizabeth M Jaffee; Lei Zheng
Journal:  Cancer Res       Date:  2016-08-05       Impact factor: 12.701

2.  DNA breaks and chromatin structural changes enhance the transcription of autoimmune regulator target genes.

Authors:  Mithu Guha; Mario Saare; Julia Maslovskaja; Kai Kisand; Ingrid Liiv; Uku Haljasorg; Tõnis Tasa; Andres Metspalu; Lili Milani; Pärt Peterson
Journal:  J Biol Chem       Date:  2017-02-27       Impact factor: 5.157

Review 3.  Constructing de novo biosynthetic pathways for chemical synthesis inside living cells.

Authors:  Amy M Weeks; Michelle C Y Chang
Journal:  Biochemistry       Date:  2011-05-26       Impact factor: 3.162

4.  TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources.

Authors:  Luca Lenzi; Federica Facchin; Francesco Piva; Matteo Giulietti; Maria Chiara Pelleri; Flavia Frabetti; Lorenza Vitale; Raffaella Casadei; Silvia Canaider; Stefania Bortoluzzi; Alessandro Coppe; Gian Antonio Danieli; Giovanni Principato; Sergio Ferrari; Pierluigi Strippoli
Journal:  BMC Genomics       Date:  2011-02-18       Impact factor: 3.969

5.  Identification of proprotein convertase substrates using genome-wide expression correlation analysis.

Authors:  Hannu Turpeinen; Sampo Kukkurainen; Kati Pulkkinen; Timo Kauppila; Kalle Ojala; Vesa P Hytönen; Marko Pesu
Journal:  BMC Genomics       Date:  2011-12-20       Impact factor: 3.969

6.  The histone methyltransferase SDG8 mediates the epigenetic modification of light and carbon responsive genes in plants.

Authors:  Ying Li; Indrani Mukherjee; Karen E Thum; Milos Tanurdzic; Manpreet S Katari; Mariana Obertello; Molly B Edwards; W Richard McCombie; Robert A Martienssen; Gloria M Coruzzi
Journal:  Genome Biol       Date:  2015-04-19       Impact factor: 13.583

7.  Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana.

Authors:  Johan Reimegård; Snehangshu Kundu; Ali Pendle; Vivian F Irish; Peter Shaw; Naomi Nakayama; Jens F Sundström; Olof Emanuelsson
Journal:  Nucleic Acids Res       Date:  2017-04-07       Impact factor: 16.971

8.  Functional Analysis of Mating Type Genes and Transcriptome Analysis during Fruiting Body Development of Botrytis cinerea.

Authors:  Sander Y A Rodenburg; Razak B Terhem; Javier Veloso; Joost H M Stassen; Jan A L van Kan
Journal:  MBio       Date:  2018-02-13       Impact factor: 7.867

9.  Genome Architecture Facilitates Phenotypic Plasticity in the Honeybee (Apis mellifera).

Authors:  Elizabeth J Duncan; Megan P Leask; Peter K Dearden
Journal:  Mol Biol Evol       Date:  2020-07-01       Impact factor: 16.240

10.  Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant Pathogen Verticillium dahliae.

Authors:  David E Torres; Bart P H J Thomma; Michael F Seidl
Journal:  Genome Biol Evol       Date:  2021-07-06       Impact factor: 3.416

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