Babel's tower revisited: a universal resource for cross-referencing across annotation databases

Drăghici, Sorin; Sellamuthu, Sivakumar; Khatri, Purvesh

doi:10.1093/bioinformatics/btl372

Cited by 37 publications

(33 citation statements)

References 30 publications

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“…5C, top) and Pathway-Express (Fig. 5C, middle) software (28)(29)(30)(31)(32)(33)(34)(35) to identify enrichment in Gene Ontology (GO) biological processes and in functional pathways, respectively. This approach suggested the probable involvement of calciummediated signaling, mitogen-activated protein kinase (MAPK), protein kinase C (PKC), and Janus-activated kinase (JAK)-signal transducer and activator of transcription (STAT) pathways in PPAPDC1B-mediated tumorigenesis.…”

Section: Cancer Researchmentioning

confidence: 99%

Characterization of the Recurrent 8p11-12 Amplicon Identifies PPAPDC1B, a Phosphatase Protein, as a New Therapeutic Target in Breast Cancer

et al. 2008

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The 8p11-12 chromosome region is one of the regions most frequently amplified in breast carcinoma (10-15% of cases). Several genes within this region have been identified as candidate oncogenes, as they are both amplified and overexpressed. However, very few studies have explored the role of these genes in cell transformation, with the aim of identifying valuable therapeutic targets. An analysis of comparative genomic hybridization array and expression profiling data for a series of 152 ductal breast carcinomas and 21 cell lines identified five genes (LSM1, BAG4, DDHD2, PPAPDC1B, and WHSC1L1) within the amplified region as consistently overexpressed due to an increased gene copy number. The use of small interfering RNA to knock down the expression of each of these genes showed the major role played by two genes, PPAPDC1B and WHSC1L1, in regulating the survival and transformation of two different cell lines harboring the 8p amplicon. The role of these two genes in cell survival and cell transformation was also confirmed by long-term knockdown expression studies using short hairpin RNAs. The potential of PPAPDC1B, which encodes a transmembrane phosphatase, as a therapeutic target was further shown by the strong inhibition of growth of breast tumor xenografts displaying 8p11-12 amplification induced by the silencing of PPAPDC1B. The oncogenic properties of PPAPDC1B were further shown by its ability to transform NIH-3T3 fibroblasts, inducing their anchorage-independent growth. Finally, microarray experiments on PPAPDC1B knockdown indicated that this gene interfered with multiple cell signaling pathways, including the Janus-activated kinase-signal transducer and activator of transcription, mitogen-activated protein kinase, and protein kinase C pathways. PPAPDC1B may also potentiate the estrogen receptor pathway by downregulating DUSP22. [Cancer Res 2008;68(17):7165-75]

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Section: Cancer Researchmentioning

confidence: 99%

Characterization of the Recurrent 8p11-12 Amplicon Identifies PPAPDC1B, a Phosphatase Protein, as a New Therapeutic Target in Breast Cancer

et al. 2008

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“…1c. In [4], Draghici et al pointed out that the accuracy of mapping depends largely on the choice of database. They also argued that in theory, these databases are supposed to provide the most up-to-date ID mapping information and cross reference each other, but they often fail to perform as expected as in the case of SMCR gene above.…”

Section: Warehouse Maintenance and Update Errorsmentioning

confidence: 99%

“…These warehouses often materialize relationships among objects represented using such IDs, which are either gathered from other databases or computed using ID mapping tools such as DAVID [3], OntoTranslate [4], Synergizer [5], GeneID Converter [6], IdBean [7], IDMapper [8], g:Profiler [9] and MatchMiner [10]. The materialized views must then be maintained by monitoring possible ID changes, migration, and relationship changes among the objects, occurring in databases they do not control, or risk producing inconsistent and obsolete results, perhaps even facing loss of functionality [11].…”

Section: Introductionmentioning

confidence: 99%

Improving Integration Effectiveness of ID Mapping Based Biological Record Linkage

Jamil

2015

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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Traditionally, biological objects such as genes, proteins, and pathways are represented by a convenient identifier, or ID, which is then used to cross reference, link and describe objects in biological databases. Relationships among the objects are often established using non-trivial and computationally complex ID mapping systems or converters, and are stored in authoritative databases such as UniGene, GeneCards, PIR and BioMart. Despite best efforts, such mappings are largely incomplete and riddled with false negatives. Consequently, data integration using record linkage that relies on these mappings produces poor quality of data, inadvertently leading to erroneous conclusions. In this paper, we discuss this largely ignored dimension of data integration, examine how the ubiquitous use of identifiers in biological databases is a significant barrier to knowledge fusion using distributed computational pipelines, and propose two algorithms for ad hoc and restriction free ID mapping of arbitrary types using online resources. We also propose two declarative statements for ID conversion and data integration based on ID mapping on-the-fly.

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“…This can be an important source of errors since up to 20% of the identifiers can be routinely lost or incorrectly mapped during identifier translations [12]. Even if the type of identifier is directly accepted, is this the native identifier used in the analysis or is an internal identifier mapping being performed?…”

Section: Reasonsmentioning

confidence: 99%

Practical Applications of the Gene Ontology Resource

Huntley

Dimmer

Apweiler

2010

Problem Solving Handbook in Computational Biology and Bioinformatics

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The Gene Ontology (GO) is a controlled vocabulary that represents knowledge about the functional attributes of gene products in a structured manner and can be used in both computational and human analyses. This vocabulary has been used by diverse curation groups to associate functional information to individual gene products in the form of annotations. GO has proven an invaluable resource for evaluating and interpreting the biological significance of large data sets, enabling researchers to create hypotheses to direct their future research. This chapter provides an overview of the Gene Ontology, how it can be used, and tips on getting the most out of GO analyses.

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Babel's tower revisited: a universal resource for cross-referencing across annotation databases

Abstract: OT is a part of Onto-Tools, which is freely available at http://vortex.cs.wayne.edu/Projects.html

Cited by 37 publications

References 30 publications

Characterization of the Recurrent 8p11-12 Amplicon Identifies PPAPDC1B, a Phosphatase Protein, as a New Therapeutic Target in Breast Cancer

Characterization of the Recurrent 8p11-12 Amplicon Identifies PPAPDC1B, a Phosphatase Protein, as a New Therapeutic Target in Breast Cancer

Improving Integration Effectiveness of ID Mapping Based Biological Record Linkage

Practical Applications of the Gene Ontology Resource

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