FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes

Al‐Shahrour, Fátima; Dı́az-Uriarte, Ramón; Dopazo, Joaquı́n

doi:10.1093/bioinformatics/btg455

Cited by 989 publications

(822 citation statements)

References 17 publications

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“…Computations and visualization were done with Cluster and TreeView software (Eisen et al, 1998), and with BRB ArrayTools v3.6.0b2 developed by Dr Richard Simon and Amy Peng Lam. The biological activity of genes with known functions was determined using the web tool FatiGO with the Gene Ontology database (Al-Shahrour et al, 2004).…”

Section: Data Analysis and Statistical Methodsmentioning

confidence: 99%

Microarray analysis refines classification of non-medullary thyroid tumours of uncertain malignancy

et al. 2007

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Section: Data Analysis and Statistical Methodsmentioning

confidence: 99%

Microarray analysis refines classification of non-medullary thyroid tumours of uncertain malignancy

et al. 2007

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“…We searched for gene ontology terms using the FatiGO tool on the Babelomics 5 platform (http://babelomics.bioinfo.cipf.es/). FatiGO 75 is an enrichment test whereby two lists of genes are compared to detect significant over-representation of functional annotations in the subject compared with the reference list. In this case, we compared the set of the 69 genes (Supplementary Table 4) associated with the 346 depth-correlated outlier SNPs detected from the Manhattan plot analyses and found within 30 kilobases of a coding gene, against the full list of 15,114 genes identified from our C. rupestris genome annotation that were associated with gene name, gene description and gene ontology terms using InterProScan.…”

Section: Screening Of Nine Populations For Outlier Snps On Contig 1041mentioning

confidence: 99%

Genomics of habitat choice and adaptive evolution in a deep-sea fish

et al. 2018

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W hile longitudinal and latitudinal habitat transitions have been proposed to define marine communities and promote intraspecific differentiation 1-3 , little is known about the importance of transitions along ocean depth gradients 4,5 , although substantial changes in species assemblages with depth have been recorded (for example, ref. 6 ), and relatively narrow depth ranges may distinguish closely related species (for example, refs 7,8 ). Understanding the relevant mechanisms will contribute significantly to our understanding of eco-evolutionary processes and the origin of marine biodiversity. We chose the roundnose grenadier (Coryphaenoides rupestris) as a model system because it is a widespread species that can inhabit a comparatively broad range of depths 9 from ~180 m to 2,600 m. It is a batch spawner, producing up to 69,000 pelagic eggs per female 10 . It has a spawning season peaking in autumn 11 (recent observations were in September at 1,500 m; ref. 12 ), preys on fish, cephalopods and invertebrates in both benthic and pelagic habitats 13 , and shows minor genetic differentiation across its geographic range [14][15][16] .Adaptation to habitat can occur among populations within a species, and if disruptive selection is associated with assortative mating has the potential to promote incipient speciation through ecological processes in sympatry 17 . When environmental change exposes new habitats and niche potential, adaptive radiations may rapidly generate a new lineage of species 18,19 . To the extent that differential selection can retain polymorphisms within or among populations, this may facilitate the process of adaptive radiation. Here, we focus on one of the key habitat transitions in the oceans-between the photic mesopelagic region and the aphotic regions below (together with the more contiguous changes associated with increasing depth). There is the potential for species (such as the roundnose grenadier), whose habitat range extends across this boundary or along the depth gradient, to experience differential selective pressures. We tested hypotheses about adaptation to these deep-sea habitats using genome sequence data together with data on the ecology and life history of the subject species. We found that juvenile fish of this species are found primarily in relatively shallow depths (near the transition between the mesopelagic and bathypelagic zones) and then migrate as they mature to different depths, and this is strongly associated with their genotype at a set of functional loci. In particular, all adults below ~1,800 m share the same homozygous genotype at each locus. There is evidence for strong selection maintaining this difference, but no clear evidence for differentiation driven by assortative mating. Results and discussionWe produced an annotated reference genome for C. rupestris with a total length of 0.829 gigabase pairs, a mean depth of 104× and an N50 of 159,738 (see Supplementary Methods for details). We used this draft genome to map 60 additional genomes sequenced to a mean depth ...

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“…bioinfo.cnio.es/; (Al-Shahrour et al, 2004)). Clusters of invasion correlated genes according to their 'Biological Process' GO terms were shown in Supplement 5.…”

Section: Establishment Of Invasion Model With Progressive Increase Inmentioning

confidence: 99%

Insulin-like growth factor binding protein-3 (IGFBP-3) acts as an invasion-metastasis suppressor in ovarian endometrioid carcinoma

et al. 2007

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Metastasis and invasion occur in the majority of epithelial ovarian carcinoma at diagnosis. To delineate the molecular signature in ovarian cancer invasion, we established and characterized a human ovarian endometrioid carcinoma (EC) cell line OVTW59-P0 and its invasion-related sublines (P1-P4, in the order of increasing invasive activity). P4 showed faster migration and larger xenograft formation with metastasis than P0. By microarray analysis of different gene expression among P0-P4 sublines, one group of gene was found negatively correlated with cancer invasion. Among these genes, IGFBP-3 was identified as one of the most remarkably suppressed gene that showed lower gene expression in P4 than P0. Re-expression of IGFBP-3 in P4 effectively inhibited cell migration, invasion and metastasis, but did not affect cell proliferation. In 35 patients with EC tumors, low IGFBP-3 expression correlated clinically with higher tumor grade, advanced stage and poor survival. Our results provide evidence and indicate that IGFBP-3 plays an important role as an invasion-metastasis suppressor in ovarian EC.

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FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes

Cited by 989 publications

References 17 publications

Microarray analysis refines classification of non-medullary thyroid tumours of uncertain malignancy

Microarray analysis refines classification of non-medullary thyroid tumours of uncertain malignancy

Genomics of habitat choice and adaptive evolution in a deep-sea fish

Insulin-like growth factor binding protein-3 (IGFBP-3) acts as an invasion-metastasis suppressor in ovarian endometrioid carcinoma

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