Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics

Damian Fermin¹ , Baxter B Allen¹ , Thomas W Blackwell¹ , Rajasree Menon¹ , Marcin Adamski¹ , Yin Xu¹ , Peter Ulintz¹ , Gilbert S Omenn² and David J States¹^,3

¹Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA

²Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA

³Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA

author email corresponding author email

Genome Biology 2006, 7:R35doi:10.1186/gb-2006-7-4-r35


Published:	28 April 2006

Subject areas: Genome studies, Bioinformatics, Methods

Additional files

Additional data file 1:

The table gives the distribution of each type of diagnostic peptide among the 128 parent genes they occur in. The columns in the table are as follows. HUGO Gene ID, HUGO Gene Identifier; Ensembl Gene ID, the Ensembl gene identifier for the gene containing the diagnostic peptides; PT, the total number of diagnostic peptides found within the coding boundaries of this gene; PM, number of perfect-matching peptides to a protein product of this gene; IE, number of intra-exonic peptides associated with this gene; OE, number of exon overlapping peptides associated with this gene; NE, number of non-exonic peptides associated with this gene; Gene Description, a short descriptor characterizing the gene. The gene description is taken from the Ensembl genome browser's record for this gene

Format: XLS Size: 41KB Download file

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Additional data file 2:

The columns of the table are as follows: PT, the total number of NR peptides associated with this gene; All, the number of peptides with EST hits; PM, number of PM peptides with EST hits; IE, the number of IE peptides with EST hits; OE, the number of OE peptides with EST hits; NE, number of NE peptides with EST hits

Format: XLS Size: 31KB Download file

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Additional data file 3:

The table columns are as follows: Peptide Type, indicates whether the anchoring peptide is an NE or OE peptide; Ensembl Gene ID, reports the gene identifier for the gene the peptide occurs in; Chr, Start, and End, report the genomic nucleotide coordinates that encode for the peptide; ESTs, reports how many ESTs overlap with these genomic coordinates

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Additional data file 4:

The columns in this spreadsheet are as follows: Ensembl Gene ID, the Ensembl gene identifier for the gene that the ORF overlaps; orflocid, a unique identifier for the ORF sequence; peplocid, a unique identifier for the peptide sequence identified as mapping to this ORF; groupId, an X!Tandem identifier for the spectrum assigned to the given peptide sequence; hyperscore, the maximum X!Tandem hyperscore assigned to this peptide; srcFile, the name of the X!Tandem file from which the peptide assignment information was extracted; peptide, the peptide sequence; orf, the complete open-reading frame sequence that the peptide matches

Format: XLS Size: 1.1MB Download file

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