The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species

Muller, Cédric; Denis, Mathieu; Gentzbittel, Laurent; Faraut, Thomas

doi:10.1093/nar/gkh460

Cited by 37 publications

(31 citation statements)

References 52 publications

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“…An external standard (plant mRNA: I11a accession number Y10291) was added to each RNA sample (1 pg for 2 mg total RNA sample) before RT to allow quantification of the cDNA production. Primers were designed using 'Primer Express' software (Applied Biosystems, Courtaboeuf, France) and the intron-exon organization of porcine genes has been deduced by comparison with human genome using Iccare software (Muller et al 2004). Translationally controlled tumour protein gene (TCTP, accession number BX667045) and COX3 gene (cytochrome c oxidase subunit III, accession number CT971556) were found to be highly expressed but not regulated during follicle development in our micro-array experiment and used as internal controls.…”

Section: Quantitative Pcr Analysis Of Gene Expressionmentioning

confidence: 99%

In vivo gene expression in granulosa cells during pig terminal follicular development

Bonnet¹,

Cao²,

SanCristobal³

et al. 2008

Reproduction

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Ovarian antral follicular development is clearly dependent on pituitary gonadotrophins FSH and LH. Although the endocrine mechanism that controls ovarian folliculogenesis leading to ovulation is quite well understood, the detailed mechanisms and molecular determinants in the different follicular compartments remain to be clarified. The aim of this study was to identify the genes differentially expressed in pig granulosa cells along the terminal ovarian follicle growth, to gain a comprehensive view of these molecular mechanisms. First, we developed a specific micro-array using cDNAs from suppression subtractive hybridization libraries (345 contigs) obtained by comparison of three follicle size classes: small, medium and large antral healthy follicles. In a second step, a transcriptomic analysis using cDNA probes from these three follicle classes identified 79 differentially expressed transcripts along the terminal follicular growth and 26 predictive genes of size classes. The differential expression of 18 genes has been controlled using real-time PCR experiments validating the micro-array analysis. Finally, the integration of the data using Ingenuity Pathways Analysis identified five gene networks providing descriptive elements of the terminal follicular development. Specifically, we observed: (1) the down-expression of ribosomal protein genes, (2) the genes involved in lipid metabolism and (3) the down-expression of cell morphology and ion-binding genes. In conclusion, this study gives new insight into the gene expression during pig terminal follicular growth in vivo and suggested, in particular, a morphological change in pig granulosa cells accompanying terminal follicular growth. Reproduction (2008) 136 211-224

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Section: Quantitative Pcr Analysis Of Gene Expressionmentioning

confidence: 99%

In vivo gene expression in granulosa cells during pig terminal follicular development

Bonnet¹,

Cao²,

SanCristobal³

et al. 2008

Reproduction

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“…Primers were designed from the EST contigs selected using the ICCARE web server (http://bioinfo.genopole-toulouse.prd.fr/iccare) (Muller et al, 2004) and primer 3 (http://frodo.wi.mit.edu/cgi-bin/ primer3/primer3_www.cgi), as described in Morisson et al (2004).…”

Section: Development Of New Est and Mrna Markers Absent From The Sequmentioning

confidence: 99%

The chicken RH map: current state of progress and microchromosome mapping

Morisson

Denis²,

Milan³

et al. 2007

Cytogenet Genome Res

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The ChickRH6 radiation hybrid panel has been used to construct consensus chromosome radiation hybrid (RH) maps of the chicken genome. Markers genotyped were either from throughout the genome or targeted to specific chromosomes and a large proportion (one third) of data was the result of collaborative efforts. Altogether, 2,531 markers were genotyped, allowing the construction of RH reference maps for 20 chromosomes and linkage groups for four other chromosomes. Amongst the markers, 581 belong to the framework maps, while 1,721 are on the comprehensive maps. Around 800 markers still have to be assigned to linkage groups. Our attempt to assign the supercontigs from the chrun (virtual chromosome containing all the genome sequence that could not be attributed to a chromosome) as well as EST (Expressed Sequence Tag) contigs that do not have a BLAST hit in the genome assembly led to the construction of new maps for microchromosomes either absent or for which very little data is present in the genome assembly. RH data is presented through our ChickRH webserver (http://chickrh.toulouse.inra.fr/), which is a mapping tool as well as the official repository RH database for genotypes. It also displays the RH reference maps and comparison charts with the sequence thus highlighting the possible discrepancies. Future improvements of the RH maps include complete coverage of the sequence assigned to chromosomes, further mapping of the chrun and mapping of EST contigs absent from the assembly. This will help finish the mapping of the smallest gene-rich microchromosomes.

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“…All publicly available chicken EST (>420 000) from Genbank and other sources [1,4,37] were collected in a local database, after which EST selection and primer design were performed after comparison to the human genome sequence using the Iccare web server [26]. EST markers corresponding to the COQ7 and DREV1 genes had been previously developed in our laboratory and were found to be linked to the GGA14 RH linkage group.…”

Section: Est (Expressed Sequence Tag) and Gene Markersmentioning

confidence: 99%

A gene-based radiation hybrid map of chicken microchromosome 14: Comparison to human and alignment to the assembled chicken sequence

et al. 2005

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-We present a gene-based RH map of the chicken microchromosome GGA14, known to have synteny conservations with human chromosomal regions HSA16p13.3 and HSA17p11.2. Microsatellite markers from the genetic map were used to check the validity of the RH map and additional markers were developed from chicken EST data to yield comparative mapping data. A high rate of intra-chromosomal rearrangements was detected by comparison to the assembled human sequence. Finally, the alignment of the RH map to the assembled chicken sequence showed a small number of discordances, most of which involved the same region of the chromosome spanning between 40.5 and 75.9 cR 6000 on the RH map.chicken / comparative mapping / radiation hybrids / microchromosome 14 / intrachromosomal rearrangement

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The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species

Cited by 37 publications

References 52 publications

In vivo gene expression in granulosa cells during pig terminal follicular development

In vivo gene expression in granulosa cells during pig terminal follicular development

The chicken RH map: current state of progress and microchromosome mapping

A gene-based radiation hybrid map of chicken microchromosome 14: Comparison to human and alignment to the assembled chicken sequence

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