scholarly journals Annotation of gene product function from high-throughput studies using the Gene Ontology

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Helen Attrill ◽  
Pascale Gaudet ◽  
Rachael P Huntley ◽  
Ruth C Lovering ◽  
Stacia R Engel ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Gene Product ◽  
High Throughput ◽  
Product Function ◽  
Gene Product Function

Test for temporal or spatial restrictions in gene product function during the cell division cycle

1983 ◽  
Vol 3 (7) ◽  
pp. 1255-1265
Author(s):  
S K Dutcher ◽  
L H Hartwell
Keyword(s):  
Cell Division ◽  
Gene Product ◽  
Gene Mutations ◽  
Cell Division Cycle ◽  
Temperature Sensitive ◽  
Restrictive Temperature ◽  
Product Function ◽  
Complete Cell ◽  
Relationship Of ◽  
Gene Product Function

The ability of a functional gene to complement a nonfunctional gene may depend upon the intracellular relationship of the two genes. If so, the function of the gene product in question must be limited in time or in space. CDC (cell division cycle) gene products of Saccharomyces cerevisiae control discrete steps in cell division; therefore, they constitute reasonable candidates for genes that function with temporal or spatial restrictions. In an attempt to reveal such restrictions, we compared the ability of a CDC gene to complement a temperature-sensitive cdc gene in diploids where the genes are located within the same nucleus to complementation in heterokaryons where the genes are located in different nuclei. In CDC X cdc matings, complementation was monitored in rare heterokaryons by assaying the production of cdc haploid progeny (cytoductants) at the restrictive temperature. The production of cdc cytoductants indicates that the cdc nucleus was able to complete cell division at the restrictive temperature and implies that the CDC gene product was provided by the other nucleus or by cytoplasm in the heterokaryon. Cytoductants from cdc28 or cdc37 crosses were not efficiently produced, suggesting that these two genes are restricted spatially or temporally in their function. We found that of the cdc mutants tested 33 were complemented; cdc cytoductants were recovered at least as frequently as CDC cytoductants. A particularly interesting example was provided by the CDC4 gene. Mutations in CDC4 were found previously to produce a defect in both cell division and karyogamy. Surprisingly, the cell division defect of cdc4 nuclei is complemented by CDC4 nuclei in a heterokaryon, whereas the karyogamy defect is not.

Rapamycin biosynthesis: elucidation of gene product function

2006 ◽  
Vol 4 (19) ◽  
pp. 3565 ◽  
Author(s):  
Matthew A. Gregory ◽  
Hui Hong ◽  
Rachel E. Lill ◽  
Sabine Gaisser ◽  
Hrvoje Petkovic ◽  
...  
Keyword(s):  
Gene Product ◽  
Product Function ◽  
Gene Product Function

ALLOANTISERUM INDUCED BLOCKADE OF IR GENE PRODUCT FUNCTION

1974 ◽  
pp. 175-190 ◽  
Author(s):  
W.E. Paul ◽  
E.M. Shevach ◽  
S.Z. Ben-Sasson ◽  
F. Finkelman ◽  
I. Green
Keyword(s):  
Gene Product ◽  
Product Function ◽  
Gene Product Function

scholarly journals Test for temporal or spatial restrictions in gene product function during the cell division cycle.

1983 ◽  
Vol 3 (7) ◽  
pp. 1255-1265 ◽  
Author(s):  
S K Dutcher ◽  
L H Hartwell
Keyword(s):  
Cell Division ◽  
Gene Product ◽  
Gene Mutations ◽  
Cell Division Cycle ◽  
Temperature Sensitive ◽  
Restrictive Temperature ◽  
Product Function ◽  
Complete Cell ◽  
Relationship Of ◽  
Gene Product Function

The ability of a functional gene to complement a nonfunctional gene may depend upon the intracellular relationship of the two genes. If so, the function of the gene product in question must be limited in time or in space. CDC (cell division cycle) gene products of Saccharomyces cerevisiae control discrete steps in cell division; therefore, they constitute reasonable candidates for genes that function with temporal or spatial restrictions. In an attempt to reveal such restrictions, we compared the ability of a CDC gene to complement a temperature-sensitive cdc gene in diploids where the genes are located within the same nucleus to complementation in heterokaryons where the genes are located in different nuclei. In CDC X cdc matings, complementation was monitored in rare heterokaryons by assaying the production of cdc haploid progeny (cytoductants) at the restrictive temperature. The production of cdc cytoductants indicates that the cdc nucleus was able to complete cell division at the restrictive temperature and implies that the CDC gene product was provided by the other nucleus or by cytoplasm in the heterokaryon. Cytoductants from cdc28 or cdc37 crosses were not efficiently produced, suggesting that these two genes are restricted spatially or temporally in their function. We found that of the cdc mutants tested 33 were complemented; cdc cytoductants were recovered at least as frequently as CDC cytoductants. A particularly interesting example was provided by the CDC4 gene. Mutations in CDC4 were found previously to produce a defect in both cell division and karyogamy. Surprisingly, the cell division defect of cdc4 nuclei is complemented by CDC4 nuclei in a heterokaryon, whereas the karyogamy defect is not.

GENE ONTOLOGY SIMILARITY MEASURES BASED ON LINEAR ORDER STATISTICS

2006 ◽  
Vol 14 (06) ◽  
pp. 639-661 ◽  
Author(s):  
JAMES M. KELLER ◽  
JAMES C. BEZDEK ◽  
MIHAIL POPESCU ◽  
NIKHIL R. PAL ◽  
JOYCE A. MITCHELL ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Order Statistics ◽  
Gene Product ◽  
Linear Order ◽  
Similarity Measures ◽  
Product Family ◽  
Amino Acid Sequences ◽  
Gene Products ◽  
Multiple Sources ◽  
Similarity Relations

The standard method for comparing gene products (proteins or RNA) is to compare their DNA or amino acid sequences. Additional information about some gene products may come from multiple sources, including the set of Gene Ontology (GO) annotations and the set of journal abstracts related to each gene product. Gene product similarity measures can be based on evaluating sets of descriptor terms found in the GO taxonomy, and/or the index term sets of the related documents (MeSH annotations). While our techniques can be applied to term sets from any taxonomy, we restrict our examples in this article to GO annotations. We investigate the use of linear order statistics (LOS) to build similarity relations on pairs of terms that are used in the GO as linguistic descriptors of genes and gene products. One of our objectives is to investigate the construction and utility of visual assessments of relational data (in this case, dissimilarity matrices) for discovering tendencies of groups of gene products to "cluster together". We use gene product data derived from a group of 194 gene products representing three protein families extracted from ENSEMBL. Our examples suggest that LOS similarity measures are more effective than traditional sequence-based similarity measures at capturing relationships between pairs of gene products in ENSEMBL families when annotation information is available. We show examples of how these similarity measures can assist in knowledge discovery and gene product family validation.

scholarly journals GOParGenPy: a high throughput method to generate Gene Ontology data matrices

2013 ◽  
Vol 14 (1) ◽  
Author(s):  
Ajay Anand Kumar ◽  
Liisa Holm ◽  
Petri Toronen
Keyword(s):  
Gene Ontology ◽  
High Throughput ◽  
High Throughput Method ◽  
Data Matrices
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