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eggNOG v4.0: nested orthology inference across 3686 organisms

Sean Powell, Kristoffer Forslund, Damian Szklarczyk, Kalliopi Trachana, Alexander Roth, Jaime Huerta-Cepas, Toni Gabaldón, Thomas Rattei, Chris Creevey, Michael Kuhn, Lars J. Jensen, Christian von Mering (+1 others)
2013 Nucleic Acids Research  
Compared with the previous version, we have more than tripled the underlying species set to cover 3686 organisms, keeping track with genome project completions while prioritizing the inclusion of high-quality  ...  We here present the fourth version of the eggNOG database (available at http://eggnog.embl.de) that derives nonsupervised orthologous groups (NOGs) from complete genomes, and then applies a comprehensive  ...  ., D.S. and A.R. generated the orthologous groups. K.F. and D.S. determined clades and performed the functional annotation. J.H. and T.G. created the alignments and  ... 
doi:10.1093/nar/gkt1253 pmid:24297252 pmcid:PMC3964997 fatcat:tppseymmmbhb5ndnyxnwoktcbq

Comparative transcriptome reveals the potential modulation mechanisms of estradiol affecting ovarian development of female Portunus trituberculatus

Meimei Liu, Jie Pan, Zhiguo Dong, Yongxu Cheng, Jie Gong, Xugan Wu, Wan-Xi Yang
2019 PLoS ONE  
This study performed transcriptome sequencing of ovary, hepatopancreas, brain ganglion, eyestalk, and mandibular organ of crabs after estradiol treatment (0.1μg g-1 crab weight).  ...  A total of 23, 806 genes were annotated, and 316, 1300, 669, 142, 383 genes were expressed differently in ovary, hepatopancreas, brain ganglion, eyestalk, and mandibular organ respectively.  ...  Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, et al. eggNOG v4.0: nested orthology inference across 3686 organisms.  ... 
doi:10.1371/journal.pone.0226698 pmid:31856263 pmcid:PMC6922394 fatcat:u7b6lr4ttbe47juzbgxlkji4te

Function and functional redundancy in microbial systems

Stilianos Louca, Martin F. Polz, Florent Mazel, Michaeline B. N. Albright, Julie A. Huber, Mary I. O'Connor, Martin Ackermann, Aria S. Hahn, Diane S. Srivastava, Sean A. Crowe, Michael Doebeli, Laura Wegener Parfrey
2018 Nature Ecology & Evolution  
result from ecological drift between equivalent organisms.  ...  On the other hand, the identity of taxa encoding each function 6 can vary substantially across space or time with little effect on the function, and this taxonomic variability 7 is frequently thought to  ...  Powell, S. et al. eggnog v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res. 331 42, D231-D239 (2014).332 [4] O'Leary, N.A. et al.  ... 
doi:10.1038/s41559-018-0519-1 pmid:29662222 fatcat:porwxpryzzegbfin4t4trqbfuq

Transcriptome Analysis of Taxillusi chinensis (DC.) Danser Seeds in Response to Water Loss

Shugen Wei, Xiaojun Ma, Limei Pan, Jianhua Miao, Jine Fu, Longhua Bai, Zhonglian Zhang, Yanhong Guan, Changming Mo, Hao Huang, Maoshan Chen, Christian Schönbach
2017 PLoS ONE  
Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, et al. eggNOG v4.0: nested orthology inference across 3686 organisms.  ...  Then, likely proteins encoded by the assembled transcripts were mapped to eggNOG database and proteins encoded by 24,580 (14.94%) transcripts were distributed in EuKaryotic Orthologous Groups (KOG), Clusters  ... 
doi:10.1371/journal.pone.0169177 pmid:28046012 pmcid:PMC5207531 fatcat:cs7nxdqqrjboznxecbhunklp2i

Dispersal strategies shape persistence and evolution of human gut bacteria

Falk Hildebrand, Toni I. Gossmann, Clémence Frioux, Ezgi Özkurt, Pernille Neve Myers, Pamela Ferretti, Michael Kuhn, Mohammad Bahram, Henrik Bjørn Nielsen, Peer Bork
2021 Cell Host and Microbe  
Powell, S., Forslund, K., Szklarczyk, D., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldó n, T., Rattei, T., Creevey, C., Kuhn, M., et al. (2014). eggNOG v4.0: nested orthology inference across 3686  ...  EggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 47, D309-D314.  ... 
doi:10.1016/j.chom.2021.05.008 pmid:34111423 pmcid:PMC8288446 fatcat:4h5p2eyjpjditbrtoowjv2toly

New insight into the gut microbiome through metagenomics

Ji B, Nielsen J
2015 Advances in Genomics and Genetics  
Powell S, Forslund K, Szklarczyk D, et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res . 2014;42(D1):D231–D239. 51.  ...  Numerous databases and online tools, such as KEGG, 49the Clusters Of Orthologous Groups database (COG), 60Pfam, 61SEED, 62eggNOG, 50MG-RAST, 63CAMERA, 64and IMG/M, 65can be used to infer the functional  ... 
doaj:becf1dc1b606466d80e46ea29725f989 fatcat:y4uqfliamzd6lbigojimkyksua

Metaepigenomic analysis reveals the unexplored diversity of DNA methylations in an environmental prokaryotic community [article]

Satoshi Hiraoka, Yusuke Okazaki, Mizue Anda, Atsushi Toyoda, Shin-ichi Nakano, Wataru Iwasaki
2018 bioRxiv   pre-print
EggNOG v4.0: Nested orthology inference across 3686 organisms. Nucleic Acids Res. 509 42, D231-D239 (2014). 510 44. UniProt Consortium.  ...  This high ratio of methylation-lacking 351 organisms contrasts remarkably with a previous report in which prokaryotic genomes were found to rarely 352 lack DNA methylation systems (<7%) 13 .  ... 
doi:10.1101/380360 fatcat:mucvb47flfc7xlyrw32uirwjqy

A study of protein coding genes in Enterobacteriaceae family: essentiality of genes and orthology [article]

Fatemeh Ashari Ghomi, University Of Canterbury
2018
We introduce an ortholog clustering algorithm that can be used to nd orthologous genes to help with annotating genomes, as well as nding the evolutionary relationships between them.  ...  J., von Mering, C., and Bork, P. (2014). eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research, 42(Database issue):D231-D239. [Pruitt et al., 2007] Pruitt, K.  ...  High-throughput studies infer information about organisms from pools of biological molecules such as DNA, RNA, protein or metabolites.  ... 
doi:10.26021/7562 fatcat:hbqvdo2kwvbwphum3t37xfwkzm

Metabolic and genomic profiling of actinobacteria strains : from new natural products to biosynthetic pathways [article]

Constanze Paulus, Universität Des Saarlandes, Universität Des Saarlandes
2019
Powell, S. et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research 42, 231-239 (2014). 30. Liu, Q. et al.  ...  The organization of the alp gene cluster lacks the co-linearity due to its unusual domain orders and domains acting across modules, which is a well-known feature of trans-AT-PKSs .  ... 
doi:10.22028/d291-27785 fatcat:vwqkllwanbd4jjhgztagrxefqu