[16] Discovering and understanding genes in human DNA sequence using GRAIL

Uberbacher, Edward C.; Xu, Ying; Mural, Richard J.

doi:10.1016/s0076-6879(96)66018-2

Cited by 127 publications

(53 citation statements)

References 15 publications

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“…Genomic sequences were analysed using GrailEXP, GENSCAN, Genie, and GenBank. GrailEXP is a gene ®nder, EST alignment utility, and exon prediction program developed at Oak Ridge National Laboratory, Oak Ridge, TN (http:// grail.lsd.ornl.gov/grailexp/) (Uberbacher et al, 1996). GENSCAN was developed in the Department of Mathematics, Stanford University, Stanford, CA (http://genes.mit.edu/GENSCAN.html) and also predicts genes and exons (Burge and Karlin, 1997).…”

Section: Computational Sequence Analysismentioning

confidence: 99%

Transcript map and complete genomic sequence for the 310 kb region of minimal allele loss on chromosome segment 11p15.5 in non-small-cell lung cancer

Zhao

Bepler

2001

Oncogene

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Molecular, functional, and clinical analyses strongly suggest that chromosome segment 11p15.5 contains a gene involved in lung cancer pathogenesis. The critical region of allele loss is 310 kb in size. We used our contig of P1-phage arti®cial chromosome (PAC) clones together with newly identi®ed bacterial arti®cial chromosome (BAC) clones and the draft human genome sequence to complete a contiguous string of 380 407 bp. Three PAC clones that span the region were used to identify transcripts by exon trapping. Computational gene prediction algorithms were used to query the sequence for potential genes and exons. Screening for expression was performed with tissue-speci®c and cell line derived mRNA arrays. The region contains the complete SSA/Ro52 and RRM1 genes, exons 7 ± 12 of the GOK gene, and the crad pseudo-gene. A cluster of six nearly identical genes with an intact open reading frame (ORF) of 585 bp that share 75% identity with the HSPC182 gene was found. In addition, ®ve putative novel genes were identi®ed. Sequence tagged sites (STS) and polymorphic markers were used to screen 117 lung cancer cell lines for homozygous deletions and none were identi®ed. These data provide the basis for the identi®cation of a lung cancer suppressor gene on 11p15.5. Oncogene (2001) 20, 8154 ± 8164.

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Section: Computational Sequence Analysismentioning

confidence: 99%

Transcript map and complete genomic sequence for the 310 kb region of minimal allele loss on chromosome segment 11p15.5 in non-small-cell lung cancer

Zhao

Bepler

2001

Oncogene

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“…In spite of this, a large fraction of genes (up to 1/3 in Saccharomyces cerevisiae and about 20% in C. elegans) must be presently classed as of "unknown" function (Vukimirovic and Tilghman 2000). In the case of prokaryotic organisms, Uberbacher et al (1996) estimate that up to 50% of the newly discovered genes have no prior homologues in existing sequence databases.…”

Section: Introductionmentioning

confidence: 99%

Ab initio gene identification: Prokaryote genome annotation with GeneScan and GLIMMER

Aggarwal

Ramaswamy

2002

J Biosci

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“…This polymorphism occurred in the PLA2A upstream region and therefore in an area where potential regulatory sequences may occur. Use of the GRAIL program 29 (through NIX, HGMP Cambridge) failed to detect POL II promoter sequences within this region.…”

mentioning

confidence: 99%

“…upstream region in transcriptional regulation of PLA2A and Seilhamer and colleagues 12 have identified a number of putative promoter motifs that occur downstream of this area. By use of the GRAIL program 29 it was possible to exclude the presence of POL II promoter sequences. Subsequent analysis of this polymorphism in the entire proband and control sample failed to support its involvement in predisposition to disease.…”

mentioning

confidence: 99%

Mutational analysis of phospholipase A2A: a positional candidate susceptibility gene for bipolar disorder

et al. 1999

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Evidence for the involvement of genetic factors in the pathogenesis of bipolar affective disorder is now well established. 1 However, the mode of inheritance is nonmendelian and this makes the identification of susceptibility loci difficult. A short-cut to localisation of a disease gene for an oligogenic/multifactorial disorder such as bipolar disorder may come from observation of cosegregation with a monogenic trait. We have described a family (pedigree 324) in which there was cosegregation of major affective disorder and Darier's disease, a dominantly inherited skin disorder, and hypothesised that this reflects genetic linkage between genes involved in these disorders. 2 Genetic mapping studies have placed the locus for Darier's disease on chromosome 12q23-q24. 3-7 We conducted subsequent linkage studies (1995) upon 45 bipolar families (without Darier's disease). These results showed some evidence in favour of linkage with chromosome 12q markers with maximum evidence at a trinucleotide repeat marker within intron 1 of the phospholipase A2A (PLA2A) gene. 8 Evidence for linkage was more significant when analysing the 22 families comprising the Cardiff centre sample, which were expected to be most genetically similar to pedigree 324.Phospholipase A2 is a superfamily of distinct enzymes 9 that play a central role in a number of cellular processes including host defence, signal transduction and phospholipid digestion/metabolism. 10 They are a diverse class of enzymes with regard to localisation, regulation, sequence, structure and role of divalent metal ions. 10 All PLA2s perform the same enzymatic reaction involving the hydrolysis of the sn-2 fatty acid acyl bond of phospholipids to yield free fatty acids and lysophospholipids and have an important role in regulation of lipid membrane fluidity. 11 Hibbeln et al 11 proposed that excess PLA2 activity disrupts membrane fluidity and composition and therefore affects the activity of membranedependent proteins, such as neurotransmitter receptoreffector complexes.In the present study mutational analysis was performed on the human PLA2A gene on chromosome 12q. Linked polymorphisms were found within exon three and the upstream region. However, the allele and genotype frequencies of these polymorphisms in samples of individuals affected with bipolar disorder (n = 96) did not differ from those of control subjects (n = 96), suggesting that these variations are not associated with bipolar affective disorder.The PLA2A gene on chromosome 12 encodes a secretory form of PLA2 found predominantly in the pancreas. 12 This might seem to make it an implausible candidate for bipolar disorder. However, it has been shown that secretory PLA2 has significant effects upon neuronal cells 13 demonstrable in vitro and thought to have significance in vivo. 14 Glutamate receptors within the brain may be involved in the mode of action of some antidepressant drugs and therefore, may be involved in the pathogenesis of depression. 15 The presence of PLA2 has been shown to accompany a modulation in me...

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[16] Discovering and understanding genes in human DNA sequence using GRAIL

Cited by 127 publications

References 15 publications

Transcript map and complete genomic sequence for the 310 kb region of minimal allele loss on chromosome segment 11p15.5 in non-small-cell lung cancer

Transcript map and complete genomic sequence for the 310 kb region of minimal allele loss on chromosome segment 11p15.5 in non-small-cell lung cancer

Ab initio gene identification: Prokaryote genome annotation with GeneScan and GLIMMER

Mutational analysis of phospholipase A2A: a positional candidate susceptibility gene for bipolar disorder

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