The BioMart community portal: an innovative alternative to large, centralized data repositories

Smedley, Damian; Haider, Syed; Durinck, Steffen; Pandini, Luca; Provero, Paolo; Allen, James; Arnaiz, Olivier; Awedh, Mohammad; Baldock, Richard; Barbiera, Giulia; Bardou, Philippe; Beck, Tim; Blake, Judith A.; Bonierbale, Merideth; Brookes, Anthony J.; Bucci, Gabriele; Buetti, Iwan; Burge, Sarah; Cabau, Cédric; Carlson, Joseph W.; Chelala, Claude; Chrysostomou, Charalambos; Cittaro, Davide; Collin, Olivier; Cordova, Raul; Cutts, Rosalind J.; Dassi, Erik; Génova, Alex Di; Djari, Anis; Esposito, Anthony L.; Estrella, Heather; Eyras, Eduardo; Fernandez-Banet, Julio; Forbes, Simon; Free, Robert C; Fujisawa, Takatomo; Gadaleta, Emanuela; García-Manteiga, José Manuel; Goodstein, David; Gray, Kristian; Guerra-Assunção, José Afonso; Haggarty, Bernard; Han, Dong Jin; Han, Byung Woo; Harris, Todd W.; Harshbarger, Jayson; Hastings, Robert K.; Hayes, Richard D.; Hoede, Claire; Hu, Shen; Hu, Zhi Liang; Hutchins, Lucie N.; Kan, Zhengyan; Kawaji, Hideya; Keliet, Aminah; Kerhornou, Arnaud; Kim, Sung Hoon; Kinsella, Rhoda; Klopp, Christophe; Kong, Lei; Lawson, Daniel; Lazarevic, Dejan; Lee, Ji Hyun; Letellier, Thomas; Li, Chuan Yun; Lió, Píetro; Liu, Chu Jun; Luo, Jie; Maass, Alejandro; Mariette, Jérôme; Maurel, Thomas; Merella, Stefania; Mohamed, Azza M.; Moreews, François; Nabihoudine, Ibounyamine; Ndegwa, Nelson; Noirot, Céline; Perez-Llamas, Cristian; Primig, Michael; Quattrone, Alessandro; Quesneville, Hadi; Rambaldi, Davide; Reecy, James M.; Riba, Michela; Rosanoff, Steven; Saddiq, Amna A.; Salas, Elisa; Sallou, Olivier; Shepherd, Rebecca; Simon, Reinhard; Sperling, Linda; Spooner, William; Staines, Daniel M.; Steinbach, Delphine; Stone, Kevin R.; Stupka, Elia; Teague, Jon W.; Ullah, Abu Z. Dayem; Wang, Jun; Ware, Doreen; Wong, Marie; Youens‐Clark, Ken; Zadissa, Amonida; Zhang, Shi Jian; Kasprzyk, Arek

doi:10.1093/nar/gkv350

Cited by 694 publications

(562 citation statements)

References 50 publications

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“…To estimate the proportion of genes encoding signaling ligands in genomes (Table 4.2), we used the BioMart portal from Ensembl (Smedley et al 2015). All the genes, which have both the following Gene Ontology (GO) annotations, "receptor binding" (Molecular Function, GO:0005102) and "extracellular region" (Cellular Component, GO:0005576), were considered as ligand genes.…”

Section: Methods: Construction Of Gephebase and Identification Of Signmentioning

confidence: 99%

Morphological Evolution Repeatedly Caused by Mutations in Signaling Ligand Genes

Martin

Courtier‐Orgogozo

2017

Diversity and Evolution of Butterfly Wing Patterns

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What types of genetic changes underlie evolution? Secreted signaling molecules (syn. ligands) can induce cells to switch states and thus largely contribute to the emergence of complex forms in multicellular organisms. It has been proposed that morphological evolution should preferentially involve changes in developmental toolkit genes such as signaling pathway components or transcription factors. However, this hypothesis has never been formally confronted to the bulk of accumulated experimental evidence. Here we examine the importance of ligandcoding genes for morphological evolution in animals. We use Gephebase (http:// www.gephebase.org), a database of genotype-phenotype relationships for evolutionary changes, and survey the genetic studies that mapped signaling genes as causative loci of morphological variation. To date, 19 signaling genes represent 20% of the cases where an animal morphological change has been mapped to a gene (80/391). This includes the signaling gene Agouti, which harbors multiple cis-regulatory alleles linked to color variation in vertebrates, contrasting with the effects of coding variation in its target, the melanocortin receptor MC1R. In sticklebacks, genetic mapping approaches have identified 4 signaling genes out of 14 loci associated with lake adaptations. Finally, in butterflies, a total of 18 allelic variants of the WntA Wnt-family ligand cause color pattern adaptations related to wing mimicry, both within and between species. We discuss possible hypotheses explaining these cases of natural replication (genetic parallelism) and conclude that signaling ligand loci are an important source of sequence variation underlying morphological change in nature.

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Section: Methods: Construction Of Gephebase and Identification Of Signmentioning

confidence: 99%

Morphological Evolution Repeatedly Caused by Mutations in Signaling Ligand Genes

Martin

Courtier‐Orgogozo

2017

Diversity and Evolution of Butterfly Wing Patterns

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“…We used a set of 10,243 genes annotated as orthologs in the six species according to Ensembl (BioMart v. 0.9) (Supplemental Table S3; Smedley et al 2015) and used 5% false-discovery rate (FDR; Benjamini-Hochberg) (Benjamini and Hochberg 1995) as our multiple-testing-corrected significance threshold. The overall analysis included five comparisons: (1) human versus each of the other five species, (2) human-specific differential expression (human vs. other five primates grouped together), (3) ape-specific differential expression (human + chimpanzee vs. other four primates), (4) Catarrhini-specific differential expression (human + chimpanzee + rhesus macaque vs. other primates), and (5) comparison between Haplorrhini (human, chimpanzee, rhesus macaque, and marmoset) and Strepsirrhini (mouse lemur and bushbaby).…”

Section: Differential Gene Expression Analysismentioning

confidence: 99%

Transposable elements are the primary source of novelty in primate gene regulation

et al. 2017

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Gene regulation shapes the evolution of phenotypic diversity. We investigated the evolution of liver promoters and enhancers in six primate species using ChIP-seq (H3K27ac and H3K4me1) to profile cis-regulatory elements (CREs) and using RNAseq to characterize gene expression in the same individuals. To quantify regulatory divergence, we compared CRE activity across species by testing differential ChIP-seq read depths directly measured for orthologous sequences. We show that the primate regulatory landscape is largely conserved across the lineage, with 63% of the tested human liver CREs showing similar activity across species. Conserved CRE function is associated with sequence conservation, proximity to coding genes, cell-type specificity, and transcription factor binding. Newly evolved CREs are enriched in immune response and neurodevelopmental functions. We further demonstrate that conserved CREs bind master regulators, suggesting that while CREs contribute to species adaptation to the environment, core functions remain intact. Newly evolved CREs are enriched in young transposable elements (TEs), including Long-Terminal-Repeats (LTRs) and SINE-VNTR-Alus (SVAs), that significantly affect gene expression. Conversely, only 16% of conserved CREs overlap TEs. We tested the cis-regulatory activity of 69 TE subfamilies by luciferase reporter assays, spanning all major TE classes, and showed that 95.6% of tested TEs can function as either transcriptional activators or repressors. In conclusion, we demonstrated the critical role of TEs in primate gene regulation and illustrated potential mechanisms underlying evolutionary divergence among the primate species through the noncoding genome.

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“…All sequences were downloaded using BioMart (Smedley et al, 2015) and loaded into Mesquite version 3.03 (Maddison and Maddison, 2015), where they were aligned using ClustalW version 2.1 (Larkin et al, 2007). FastTree version 2.1.7 (Price et al, 2010) was used to create an approximate maximum-likelihood phylogenetic tree from the aligned sequences.…”

Section: Phylogenetic Analyses and In Silico Analysis Of Expression Datamentioning

confidence: 99%

nana plant2 Encodes a Maize Ortholog of the Arabidopsis Brassinosteroid Biosynthesis Gene DWARF1, Identifying Developmental Interactions between Brassinosteroids and Gibberellins

et al. 2016

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A small number of phytohormones dictate the pattern of plant form affecting fitness via reproductive architecture and the plant's ability to forage for light, water, and nutrients. Individual phytohormone contributions to plant architecture have been studied extensively, often following a single component of plant architecture, such as plant height or branching. Both brassinosteroid (BR) and gibberellin (GA) affect plant height, branching, and sexual organ development in maize (Zea mays). We identified the molecular basis of the nana plant2 (na2) phenotype as a loss-of-function mutation in one of the two maize paralogs of the Arabidopsis (Arabidopsis thaliana) BR biosynthetic gene DWARF1 (DWF1). These mutants accumulate the DWF1 substrate 24-methylenecholesterol and exhibit decreased levels of downstream BR metabolites. We utilized this mutant and known GA biosynthetic mutants to investigate the genetic interactions between BR and GA. Double mutants exhibited additivity for some phenotypes and epistasis for others with no unifying pattern, indicating that BR and GA interact to affect development but in a context-dependent manner. Similar results were observed in double mutant analyses using additional BR and GA biosynthetic mutant loci. Thus, the BR and GA interactions were neither locus nor allele specific. Exogenous application of GA 3 to na2 and d5, a GA biosynthetic mutant, also resulted in a diverse pattern of growth responses, including BR-dependent GA responses. These findings demonstrate that BR and GA do not interact via a single inclusive pathway in maize but rather suggest that differential signal transduction and downstream responses are affected dependent upon the developmental context.

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The BioMart community portal: an innovative alternative to large, centralized data repositories

Cited by 694 publications

References 50 publications

Morphological Evolution Repeatedly Caused by Mutations in Signaling Ligand Genes

Morphological Evolution Repeatedly Caused by Mutations in Signaling Ligand Genes

Transposable elements are the primary source of novelty in primate gene regulation

nana plant2 Encodes a Maize Ortholog of the Arabidopsis Brassinosteroid Biosynthesis Gene DWARF1, Identifying Developmental Interactions between Brassinosteroids and Gibberellins

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