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GLAD: an Online Database of Gene List Annotation for Drosophila.

Hu Y, Comjean A, Perkins LA, Perrimon N, Mohr SE - J Genomics (2015)

Bottom Line: The resource is available online for scientists to search and view, and is editable based on community input.We anticipate that the number of lists will increase over time; that the composition of some lists will grow and/or change over time as new information becomes available; and that the lists will benefit the scientific community, e.g. at experimental design and data analysis stages.Based on this, we present an easily updatable online database, available at www.flyrnai.org/glad, at which gene group lists can be viewed, searched and downloaded.

View Article: PubMed Central - PubMed

Affiliation: 1. Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.

ABSTRACT
We present a resource of high quality lists of functionally related Drosophila genes, e.g. based on protein domains (kinases, transcription factors, etc.) or cellular function (e.g. autophagy, signal transduction). To establish these lists, we relied on different inputs, including curation from databases or the literature and mapping from other species. Moreover, as an added curation and quality control step, we asked experts in relevant fields to review many of the lists. The resource is available online for scientists to search and view, and is editable based on community input. Annotation of gene groups is an ongoing effort and scientific need will typically drive decisions regarding which gene lists to pursue. We anticipate that the number of lists will increase over time; that the composition of some lists will grow and/or change over time as new information becomes available; and that the lists will benefit the scientific community, e.g. at experimental design and data analysis stages. Based on this, we present an easily updatable online database, available at www.flyrnai.org/glad, at which gene group lists can be viewed, searched and downloaded.

No MeSH data available.


Strategy for assembly of a Drosophila kinases gene group. As outlined, we incorporated information from several sources. See main text and Table 1 for relevant URLs and reference citations.
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Figure 1: Strategy for assembly of a Drosophila kinases gene group. As outlined, we incorporated information from several sources. See main text and Table 1 for relevant URLs and reference citations.

Mentions: As mentioned above, several gene groups were annotated in conjunction with release of the Drosophila genome in 2000 (see for example 5-8). More recently, FlyBase has begun to associate a number of genes with gene groups. The first release of the FlyBase gene groups (FB2015_02, released May 4, 2015) includes 178 gene groups, with the number of genes in a group ranging from 1 to 168. As we had high-throughput functional genomics screening in mind, the approaches we took to defining, building and annotating gene groups draw on knowledge not available in 2000 and are complementary to the approaches taken by FlyBase. In general, our focus is on larger sets of genes and, given the goals of large-scale functional genomics, we tend to cast a broader net, applying less stringent cut-offs for inclusion in a gene group. So far, we have annotated 23 major gene groups with 29 sub-groups. For example, kinases are annotated as belonging to one of two subgroups: protein kinases and non-protein kinases, and the transcription factors (TFs), related proteins and other DNA-binding proteins are organized into four groups, DNA-binding with transcription factor activity; transcriptional co-factors; chromatin regulation; and possible TFs, which we assign to proteins predicted to be TF based only on low confidence data (Table 1). The number of genes in major gene groups ranges from 53 to 3,683. Currently, GO annotation is the major resource for identification of groups of genes relevant to a particular molecular function, biological process or sub-cellular localization. Several individual laboratories have also built databases in particular areas (e.g. GlycoFly 9 and FlyTF 10). In addition, a large amount of information exists in free text format in the literature. Although our strategy differed for each group, depending on available resources, in general we built the lists using one or more of the following approaches: a) mining of organized and digitalized information from existing annotation resources and databases including generic gene and protein annotation, e.g. gene ontology and UniProt, as well as specialized resources, e.g. transporterDB 11 or FlyTF 10, 12; b) mining of information in free text format from the literature; c) mining lists from relevant publications on Drosophila or other species; d) direct curation or review by experts (Table 1). The strategy used to build a Drosophila kinases gene group is outlined in Fig. 1. To help guide studies or analyses that use the gene groups, when possible we have assigned confidence scores that help separate high- and low-confidence associations of a gene with a given group. See Methods and Table 1 for additional details regarding annotation.


GLAD: an Online Database of Gene List Annotation for Drosophila.

Hu Y, Comjean A, Perkins LA, Perrimon N, Mohr SE - J Genomics (2015)

Strategy for assembly of a Drosophila kinases gene group. As outlined, we incorporated information from several sources. See main text and Table 1 for relevant URLs and reference citations.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4495321&req=5

Figure 1: Strategy for assembly of a Drosophila kinases gene group. As outlined, we incorporated information from several sources. See main text and Table 1 for relevant URLs and reference citations.
Mentions: As mentioned above, several gene groups were annotated in conjunction with release of the Drosophila genome in 2000 (see for example 5-8). More recently, FlyBase has begun to associate a number of genes with gene groups. The first release of the FlyBase gene groups (FB2015_02, released May 4, 2015) includes 178 gene groups, with the number of genes in a group ranging from 1 to 168. As we had high-throughput functional genomics screening in mind, the approaches we took to defining, building and annotating gene groups draw on knowledge not available in 2000 and are complementary to the approaches taken by FlyBase. In general, our focus is on larger sets of genes and, given the goals of large-scale functional genomics, we tend to cast a broader net, applying less stringent cut-offs for inclusion in a gene group. So far, we have annotated 23 major gene groups with 29 sub-groups. For example, kinases are annotated as belonging to one of two subgroups: protein kinases and non-protein kinases, and the transcription factors (TFs), related proteins and other DNA-binding proteins are organized into four groups, DNA-binding with transcription factor activity; transcriptional co-factors; chromatin regulation; and possible TFs, which we assign to proteins predicted to be TF based only on low confidence data (Table 1). The number of genes in major gene groups ranges from 53 to 3,683. Currently, GO annotation is the major resource for identification of groups of genes relevant to a particular molecular function, biological process or sub-cellular localization. Several individual laboratories have also built databases in particular areas (e.g. GlycoFly 9 and FlyTF 10). In addition, a large amount of information exists in free text format in the literature. Although our strategy differed for each group, depending on available resources, in general we built the lists using one or more of the following approaches: a) mining of organized and digitalized information from existing annotation resources and databases including generic gene and protein annotation, e.g. gene ontology and UniProt, as well as specialized resources, e.g. transporterDB 11 or FlyTF 10, 12; b) mining of information in free text format from the literature; c) mining lists from relevant publications on Drosophila or other species; d) direct curation or review by experts (Table 1). The strategy used to build a Drosophila kinases gene group is outlined in Fig. 1. To help guide studies or analyses that use the gene groups, when possible we have assigned confidence scores that help separate high- and low-confidence associations of a gene with a given group. See Methods and Table 1 for additional details regarding annotation.

Bottom Line: The resource is available online for scientists to search and view, and is editable based on community input.We anticipate that the number of lists will increase over time; that the composition of some lists will grow and/or change over time as new information becomes available; and that the lists will benefit the scientific community, e.g. at experimental design and data analysis stages.Based on this, we present an easily updatable online database, available at www.flyrnai.org/glad, at which gene group lists can be viewed, searched and downloaded.

View Article: PubMed Central - PubMed

Affiliation: 1. Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.

ABSTRACT
We present a resource of high quality lists of functionally related Drosophila genes, e.g. based on protein domains (kinases, transcription factors, etc.) or cellular function (e.g. autophagy, signal transduction). To establish these lists, we relied on different inputs, including curation from databases or the literature and mapping from other species. Moreover, as an added curation and quality control step, we asked experts in relevant fields to review many of the lists. The resource is available online for scientists to search and view, and is editable based on community input. Annotation of gene groups is an ongoing effort and scientific need will typically drive decisions regarding which gene lists to pursue. We anticipate that the number of lists will increase over time; that the composition of some lists will grow and/or change over time as new information becomes available; and that the lists will benefit the scientific community, e.g. at experimental design and data analysis stages. Based on this, we present an easily updatable online database, available at www.flyrnai.org/glad, at which gene group lists can be viewed, searched and downloaded.

No MeSH data available.