The Gene Ontology project in 2008

Harris, Midori A.; Deegan, Jennifer; Ireland, Amelia; Lomax, Jane; Ashburner, Michael; Tweedie, Susan; Carbon, Seth; Lewis, Suzanna; Mungall, Chris; Richter, J; Eilbeck, Karen; Blake, Judith A.; Bult, Carol J.; Diehl, Alexander D.; Dolan, M. Eileen; Drabkin, Harold J.; Eppig, Janan T.; Hill, David P.; Ni, Li; Ringwald, Martin; Balakrishnan, Rama; Binkley, Gail; Cherry, J. Michael; Christie, Karen R.; Costanzo, Maria C.; Dong, Qing; Engel, Stacia R.; Fisk, Dianna G.; Hirschman, Jodi E.; Hitz, Benjamin; Hong, Eurie L.; Krieger, Cynthia J.; Miyasato, Stuart R.; Nash, Robert S.; Park, Julie; Skrzypek, Marek S.; Weng, Shuai; Wong, Edith D.; Zhu, Kathy K.; Botstein, David; Dolinski, Kara; Livstone, Michael S.; Oughtred, Rose; Berardini, Tanya Z.; Li, Donghui; Rhee, Seung Y.; Apweiler, Rolf; Barrell, Daniel; Camon, Evelyn; Dimmer, Emily; Huntley, Rachael P.; Mulder, Nicola; Khodiyar, Varsha; Lovering, Ruth C.; Povey, Sue; Chisholm, Rex L.; Fey, Petra; Gaudet, Pascale; Kibbe, Warren A.; Kishore, Ranjana; Schwarz, Erich M.; Sternberg, Paul W.; Auken, Kimberly Van; Giglio, Michelle; Hannick, Linda; Wortman, Jennifer; Aslett, Martin; Berriman, Matthew; Wood, Valerie; Jacob, Howard J.; Laulederkind, Stan; Petri, Victoria; Shimoyama, Mary; Smith, Jennifer S.; Twigger, Simon; Jaiswal, Pankaj; Seigfried, Trent E.; Howe, Doug; Westerfield, Monte; Collmer, Candace Whitmer; Alalibo, Trudy Torto; Feltrin, Erika; Valle, Giorgio; Bromberg, Susan K.; Burgess, Shane C.; McCarthy, Fiona M.

doi:10.1093/nar/gkm883

Cited by 671 publications

(285 citation statements)

References 17 publications

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“…Gene Ontology (GO) is an annotation framework that uses a controlled vocabulary to assign functional attributes to genes and gene products from any organism (Consortium 2008). GO consists of three controlled ontologies divided into molecular function, biological process and cellular component that can allow insight into the functional differences between cDNA populations.…”

Section: Assigning Gene Ontologies To the Ssh Derived Estsmentioning

confidence: 99%

Transcriptome analysis during somatic embryogenesis of the tropical monocot Elaeis guineensis: evidence for conserved gene functions in early development

et al. 2009

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With the aim of understanding the molecular mechanisms underlying somatic embryogenesis (SE) in oil palm, we examined transcriptome changes that occur when embryogenic suspension cells are initiated to develop somatic embryos. Two reciprocal suppression subtractive hybridization (SSH) libraries were constructed from oil palm embryogenic cell suspensions: one in which embryo development was blocked by the presence of the synthetic auxin analogue 2,4-dichlorophenoxyacetic acid (2,4-D: ) in the medium (proliferation library); and another in which cells were stimulated to form embryos by the removal of 2,4-D: from the medium (initiation library). A total of 1867 Expressed Sequence Tags (ESTs) consisting of 1567 potential unigenes were assembled from the two libraries. Functional annotation indicated that 928 of the ESTs correspond to proteins that have either no similarity to sequences in public databases or are of unknown function. Gene Ontology (GO) terms assigned to the two EST populations give clues to the underlying molecular functions, biological processes and cellular components involved in the initiation of embryo development. Macroarrays were used for transcript profiling the ESTs during SE. Hierarchical cluster analysis of differential transcript accumulation revealed 4 distinct profiles containing a total of 192 statistically significant developmentally regulated transcripts. Similarities and differences between the global results obtained with in vitro systems from dicots, monocots and gymnosperms will be discussed.

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Section: Assigning Gene Ontologies To the Ssh Derived Estsmentioning

confidence: 99%

Transcriptome analysis during somatic embryogenesis of the tropical monocot Elaeis guineensis: evidence for conserved gene functions in early development

et al. 2009

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“…Gene ontology (GO) [18] functional enrichment analysis, in the categories cellular component, molecular function and biological process, was performed for the predicted target genes of differentially expressed miRNAs. Kyoto Encyclopedia of Genes and Genomes (KEGG, www.genome.jp/kegg/) pathway enrichment [19] was also performed for the predicted target genes (FDR <0.05).…”

Section: Methodsmentioning

confidence: 99%

Investigation of microRNA Expression Profiles Associated with Human Alcoholic Cardiomyopathy

Jing

Jin

Lü³

et al. 2015

Cardiology

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Objectives: We aimed to investigate the differentially expressed microRNAs (miRNAs) and their target genes in human alcoholic cardiomyopathy (ACM). Methods: The expression levels of plasma miRNAs of 78 male ACM patients and 78 healthy men were detected by using the 6th-generation miRCURY™ LNA array (v.16.0). The prediction analysis for microarrays (PAM) method was used to identify the differentially expressed miRNAs. Target genes of the identified differentially expressed miRNAs were predicted using TargetScan 5.2 and Miranda. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to perform functional annotation and pathway enrichment analysis of target genes respectively, followed by real-time RT-PCR analysis to validate the expression changes of miRNAs. Results: Twenty-one differentially expressed miRNAs were identified. Nine differentially expressed miRNAs (hsa-miR-506, hsa-miR-1285, hsa-miR-512-3P, hsa-miR-138, hsa-miR-485-5P, hsa-miR-4262, hsa-miR-548c-3P, has-miR-548a-5P and kshv-miR-K12-1), involved in multiple functions and pathways, were selected for real-time RT-PCR confirmation. Moreover, two significantly important subpathways (neurotrophin signaling pathway and inositol phosphate metabolism) were predicted. Conclusion: The screened differentially expressed miRNAs may be involved in the development of ACM. Specific miRNAs, such as miR-138, may be considered as a new target for the early diagnosis and treatment of human ACM.

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“…Gene Ontology (GO) is an internationally standardized gene function classification system that provides a dynamic standard vocabulary and a strictly defined concept to describe the functional attributes of genes and their products [50]. In order to classify the putative functions of the predicted Chinese fir genes, the assembled unigene sequences were uploaded into the GO database.…”

Section: Go Assignmentsmentioning

confidence: 99%

Transcriptome Characterization of the Chinese Fir (Cunninghamia lanceolata (Lamb.) Hook.) and Expression Analysis of Candidate Phosphate Transporter Genes

et al. 2017

Forests

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Abstract:Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is the most important afforestation tree species in China because of its excellent timber quality and high yield. However, the limited availability of phosphorus in forest soils is widespread and has become an important factor in the declining productivity of Chinese fir plantations. Here we used the Illumina HiSeq™ 2000 DNA sequencing platform to sequence root, stem, and leaf transcriptomes of one-year old Chinese fir clones with phosphorus treatment. Approximately 236,529,278 clean reads were obtained and generated 35.47 G of sequencing data. These reads were assembled into 413,806 unigenes with a mean length of 520 bp. In total, 109,596 unigenes were annotated in the NR (NCBI non-redundant) database, 727,287 genes were assigned for GO (Gene Ontology) terms, information for 92,001 classified unigenes was assigned to 26 KOG (Karyotic Orthologous Groups) categories, and 57,042 unigenes were significantly matched with 132 KEGG (Kyoto Encyclopedia of Genes and Genomes) predicted pathways. In total, 49 unigenes were identified as exhibiting inorganic phosphate transporter activity, and 14 positive genes' expression patterns in different phosphorus deficiency treatments were analyzed by qRT-PCR to explore their putative functions. This study provides a basic foundation for functional genomic studies of the phosphate transporter in Chinese fir, and also presents an extensive annotated sequence resource for molecular research.

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The Gene Ontology project in 2008

Cited by 671 publications

References 17 publications

Transcriptome analysis during somatic embryogenesis of the tropical monocot Elaeis guineensis: evidence for conserved gene functions in early development

Transcriptome analysis during somatic embryogenesis of the tropical monocot Elaeis guineensis: evidence for conserved gene functions in early development

Investigation of microRNA Expression Profiles Associated with Human Alcoholic Cardiomyopathy

Transcriptome Characterization of the Chinese Fir (Cunninghamia lanceolata (Lamb.) Hook.) and Expression Analysis of Candidate Phosphate Transporter Genes

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