Ensembl 2018

Zerbino, Daniel R.; Achuthan, Premanand; Akanni, Wasiu; Amode, M Ridwan; Barrell, Daniel; Bhai, Jyothish; Billis, Konstantinos; Cummins, Carla; Gall, Astrid; Girón, Carlos García; Gil, Laurent; Gordon, Leo I.; Haggerty, Leanne; Haskell, Erin; Hourlier, Thibaut; Izuogu, Osagie; Janacek, Sophie H; Juettemann, Thomas; To, Jimmy Kiang; Laird, Matthew R.; Lavidas, Ilias; Liu, Zhicheng; Loveland, Jane; Maurel, Thomas; McLaren, William; Moore, Benjamin; Mudge, Jonathan M.; Murphy, Daniel N.; Newman, Victoria L.; Nuhn, Michael; Ogeh, Denye; Ong, Chuang Kee; Parker, Anne; Patrício, Mateus; Riat, Harpreet Singh; Schuilenburg, Helen; Sheppard, Dan; Sparrow, Helen; Taylor, Kieron; Thormann, Anja; Vullo, Alessandro; Walts, Brandon; Zadissa, Amonida; Frankish, Adam; Hunt, Sarah; Kostadima, Myrto; Langridge, Nicholas; Martin, Fergal J.; Muffato, Matthieu; Perry, Emily; Ruffier, Magali; Staines, Daniel M.; Trevanion, Stephen J.; Aken, Bronwen; Cunningham, Fiona; Yates, Andy; Flicek, Paul

doi:10.1093/nar/gkx1098

Cited by 2,589 publications

(2,363 citation statements)

References 37 publications

Supporting

Mentioning

2,288

Contrasting

Unclassified

Order By: Relevance

“…Pokorná et al, 2011;O'Meally et al, 2012]. We performed BLAST of the assembled female-specific RAD contigs to the chicken transcriptome (using Ensembl [Zerbino et al, 2018]), implemented in Geneious (v10) [Kearse et al, 2012] with a maximum E-value cutoff of 1e -50 and word size of 15 bp.…”

Section: Using the Qiagenmentioning

confidence: 99%

ZZ/ZW Sex Chromosomes in the Endemic Puerto Rican Leaf-Toed Gecko (Phyllodactylus wirshingi)

Nielsen

Daza

Pinto

et al. 2019

Cytogenet Genome Res

View full text Add to dashboard Cite

Investigating the evolutionary processes influencing the origin, evolution, and turnover of vertebrate sex chromosomes requires the classification of sex chromosome systems in a great diversity of species. Among amniotes, squamates (lizards and snakes) - and gecko lizards in particular - are worthy of additional study. Geckos possess all major vertebrate sex-determining systems, as well as multiple transitions among them, yet we still lack data on the sex-determining systems for the vast majority of species. We here utilize restriction-site associated DNA sequencing (RADseq) to identify the sex chromosome system of the Puerto Rican endemic leaf-toed gecko (Phyllodactylidae: Phyllodactylus wirshingi), in order to confirm a ZZ/ZW sex chromosome system within the genus, as well as to better categorize the diversity within this poorly characterized family. RADseq has proven an effective alternative to cytogenetic methods for determining whether a species has an XX/XY or ZZ/ZW sex chromosome system - particularly in taxa with non-differentiated sex chromosomes - but can also be used to identify which chromosomes in the genome are the sex chromosomes. We here identify a ZZ/ZW sex chromosome system in P. wirshingi. Furthermore, we show that 4 of the female-specific markers contain fragments of genes found on the avian Z and discuss homology with P. wirshingi sex chromosomes.

show abstract

Section: Using the Qiagenmentioning

confidence: 99%

ZZ/ZW Sex Chromosomes in the Endemic Puerto Rican Leaf-Toed Gecko (Phyllodactylus wirshingi)

Nielsen

Daza

Pinto

et al. 2019

Cytogenet Genome Res

View full text Add to dashboard Cite

show abstract

“…It is desirable to test and apply our method on the data from other sources. We therefore searched for the relevant data from other databases including Gene Expression Omnibus (GEO) [62], Ensembl [63], Hugo Gene Nomenclature Committee (HGNC) [64], ArrayExpress [65], and Catalogue of Somatic Mutations in Cancer (COSMIC) [66]. These databases provide comprehensive genome data for colon cancer, such as gene expression dataset, somatic mutation dataset and gene location dataset even gene Methylation dataset.…”

Section: Discussionmentioning

confidence: 99%

Exploration of immunogene in colon cancer recurrence

Sun¹,

Yao²,

Yuan³

et al. 2018

Oncotarget

View full text Add to dashboard Cite

Colon adenocarcinoma is the third most common cancer with high risk of recurrence and deteriorative consequences. Given the importance of immune genes in tumor regulation and cancer immunotherapy, there is a need to comprehensively profile the immunoregulatory genes from multiple types of colon cancer patient genomic data for discovering important associations and potential therapeutic targets of colon cancer recurrence. We used publicly available colon tumor tissue genomic data from The Cancer Genome Atlas database and immune genes data from innateDB database in this study. We derived the immune genes profiles by exploring multiple genomic profiles (gene expression, clinical and somatic mutation) in colon cancer. Some of the synthetic lethal genes we identified, such as CASP14, MS4A6E, KIR2DL1, KIR3DL1, KIR2DL3, CCL1, IL36B, FOXO3, POU2F1, SMAD3, HOXA9, PACS1, PROM1, DIDO1, SRC, CBFA2T2, NCOA6, PGAM1 and PROC, have been suggested to be potential targets correlated with immune genes for colon cancer recurrence treatment. Moreover, TLR2 could be promisingly new early stage indicator for colon adenocarcinoma recurrence. This is a systematic study that combines three different types of genomic data to molecularly characterize colon cancer and aims to identify potential targets for colon adenocarcinoma therapy. Meanwhile, the integrative analysis of immune genes for colon cancer could assist in identifying potential new symbols for colon adenocarcinoma recurrence.

show abstract

“…iORF aligned coordinates were then converted to genomic coordinates on the respective genomes of each strain, and removed if there was any overlap with a known feature annotation, such as rRNA, a tRNA, a ncRNA, a snoRNA, non-conserved genes and pseudogenes annotated on the reference S288C (version R64-2-1 https://www.yeastgenome.org/). Additional masking was performed by removing iORFs i) located in a region with more than 0.6 % of sequence identity with S. cerevisiae ncRNA or gene (including pseudogenes and excluding dubious ORFs) from the reference genome, or Saccharomyces kudriavzevii and Saccharomyces eubayanus genes (Zerbino et al 2018), ii) in a low complexity region identified with repeat masker (http://www.repeatmasker.org/) and iii) when local alignments of iORFs +/-300 bp displayed less than 60% of identity (including gaps). If an .…”

Section: Iorf Annotation and Conservation Levelmentioning

confidence: 99%

The high turnover of ribosome-associated transcripts fromde novoORFs produces gene-like characteristics available forde novogene emergence in wild yeast populations

Durand

Gagnon‐Arsenault

Hatin

et al. 2018

Preprint

View full text Add to dashboard Cite

Little is known about the rate of emergence of genes de novo, how they spread in populations and what their initial properties are. We examined wild Saccharomyces paradoxus populations to characterize the diversity and turnover of intergenic ORFs over short evolutionary time-scales. We identified ~34,000 intergenic ORFs per individual genome for a total of ~64,000 orthogroups, which resulted from an estimated turnover rate relatively smaller than the rate of gene duplication in yeast. Hundreds of intergenic ORFs show translation signatures, similar to canonical genes, but lower translation efficiency, which could reduce their potential production cost or simply reflect a lack of optimization. Translated intergenic ORFs tend to display low expression levels with sequence properties that are on average closer to expectations based on intergenic sequences.However, some predicted de novo polypeptides with gene-like properties emerged from ancient as well as recent birth events, illustrating that the raw material for functional innovations may appear even over short evolutionary time-scales. Our results suggest that variation in the mutation rate along the genome impacts the turnover of random polypeptides, which may in turn influence their early evolutionary trajectory. Whereas low mutation rate regions allow more time for random intergenic ORFs to evolve and become functional before being lost, mutation hotspots allow for the rapid exploration of the molecular landscape, thereby increasing the probability to acquire a polypeptide with immediate gene-like properties and thus functional potential.

show abstract

Ensembl 2018

Cited by 2,589 publications

References 37 publications

ZZ/ZW Sex Chromosomes in the Endemic Puerto Rican Leaf-Toed Gecko (<b><i>Phyllodactylus wirshingi</i></b>)

ZZ/ZW Sex Chromosomes in the Endemic Puerto Rican Leaf-Toed Gecko (<b><i>Phyllodactylus wirshingi</i></b>)

Exploration of immunogene in colon cancer recurrence

The high turnover of ribosome-associated transcripts fromde novoORFs produces gene-like characteristics available forde novogene emergence in wild yeast populations

Contact Info

Product

Resources

About