MassNet: a functional annotation service for protein mass spectrometry data

Park, Daeui; Kim, Byoung-Chul; Cho, Seong-Woong; Park, Seong-Jin; Choi, Jong-Soon; Kim, Kyung Sik; Bhak, Jong; Lee, Sunghoon

doi:10.1093/nar/gkn241

Cited by 9 publications

(6 citation statements)

References 28 publications

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“…In addition, despite the fact that the brain exhibits one of the most complex transcriptomes, dynamic range of mRNA expression might be high enough to warrant normalization before de novo sequencing. Second, identifying the presence of genes and transcripts does not equate with building a phylome, that is , the complete set of gene family trees across species (as performed in Ensembl [85] or the PhylomeDB [86]). Phylomes are of great interest in evolutionary biology because they allow rigorous differentiation of orthologs and paralogs, hence, the identification of gene gains, duplications, and losses on the species phylogenetic tree [47,87], as well as the investigation of gene expression evolution [88-90].…”

Section: Discussionmentioning

confidence: 99%

Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles

Tzika

Helaers

Schramm

et al. 2011

EvoDevo

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BackgroundReptiles are largely under-represented in comparative genomics despite the fact that they are substantially more diverse in many respects than mammals. Given the high divergence of reptiles from classical model species, next-generation sequencing of their transcriptomes is an approach of choice for gene identification and annotation.ResultsHere, we use 454 technology to sequence the brain transcriptome of four divergent reptilian and one reference avian species: the Nile crocodile, the corn snake, the bearded dragon, the red-eared turtle, and the chicken. Using an in-house pipeline for recursive similarity searches of >3,000,000 reads against multiple databases from 7 reference vertebrates, we compile a reptilian comparative transcriptomics dataset, with homology assignment for 20,000 to 31,000 transcripts per species and a cumulated non-redundant sequence length of 248.6 Mbases. Our approach identifies the majority (87%) of chicken brain transcripts and about 50% of de novo assembled reptilian transcripts. In addition to 57,502 microsatellite loci, we identify thousands of SNP and indel polymorphisms for population genetic and linkage analyses. We also build very large multiple alignments for Sauropsida and mammals (two million residues per species) and perform extensive phylogenetic analyses suggesting that turtles are not basal living reptiles but are rather associated with Archosaurians, hence, potentially answering a long-standing question in the phylogeny of Amniotes.ConclusionsThe reptilian transcriptome (freely available at http://www.reptilian-transcriptomes.org) should prove a useful new resource as reptiles are becoming important new models for comparative genomics, ecology, and evolutionary developmental genetics.

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Section: Discussionmentioning

confidence: 99%

Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles

Tzika

Helaers

Schramm

et al. 2011

EvoDevo

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“…PCC 6803 and Xanthomonas oryzae , have been published to map the whole protein-protein interaction networks [ 3 , 4 ]. Thanks to advanced high-throughput PPI experiments and information technology, many biologists can access large-scale species specific PPI data on the web [ 5 ]. Several web sites have been developed to disseminate PPI data such as POINT [ 6 ], OPHID [ 7 ], and PIANA [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440

et al. 2009

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BackgroundPseudomonas putida KT2440 (P. putida KT2440) is a highly versatile saprophytic soil bacterium. It is a certified bio-safety host for transferring foreign genes. Therefore, the bacterium is used as a model organism for genetic and physiological studies and for the development of biotechnological applications. In order to provide a more systematic application of the organism, we have constructed a protein-protein interaction (PPI) network analysis system of P. putida KT2440.ResultsPutidaNET is a comprehensive interaction database and server of P. putida KT2440 which is generated from three protein-protein interaction (PPI) methods. We used PSIMAP (Protein Structural Interactome MAP), PEIMAP (Protein Experimental Interactome MAP), and Domain-domain interactions using iPfam. PutidaNET contains 3,254 proteins, and 82,019 possible interactions consisting of 61,011 (PSIMAP), 4,293 (PEIMAP), and 30,043 (iPfam) interaction pairs except for self interaction. Also, we performed a case study by integrating a protein interaction network and experimental 1-DE/MS-MS analysis data P. putida. We found that 1) major functional modules are involved in various metabolic pathways and ribosomes, and 2) existing PPI sub-networks that are specific to succinate or benzoate metabolism are not in the center as predicted.ConclusionWe introduce the PutidaNET which provides predicted interaction partners and functional analyses such as physicochemical properties, KEGG pathway assignment, and Gene Ontology mapping of P. putida KT2440 PutidaNET is freely available at http://sequenceome.kobic.kr/PutidaNET.

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“…Ortho-Profile, owing to the iterative approach combined with the high sensitivity of profile-to-sequence and HMM-to-HMM searches, allows detection of even remote orthologs and thus complements other large-scale orthology prediction systems. In-paranoid [44], Ortho-MCL [45] and phylogeny-based orthology determination [46,47] are applicable for orthology reconstruction when homology is detectable at the protein sequence level. For more divergent proteins, homology detection based on sequence-profiles is sometimes used (including the presence of PFAM domains) or overlooked.…”

Section: Discussionmentioning

confidence: 99%

Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase

et al. 2012

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BackgroundOrthology is a central tenet of comparative genomics and ortholog identification is instrumental to protein function prediction. Major advances have been made to determine orthology relations among a set of homologous proteins. However, they depend on the comparison of individual sequences and do not take into account divergent orthologs.ResultsWe have developed an iterative orthology prediction method, Ortho-Profile, that uses reciprocal best hits at the level of sequence profiles to infer orthology. It increases ortholog detection by 20% compared to sequence-to-sequence comparisons. Ortho-Profile predicts 598 human orthologs of mitochondrial proteins from Saccharomyces cerevisiae and Schizosaccharomyces pombe with 94% accuracy. Of these, 181 were not known to localize to mitochondria in mammals. Among the predictions of the Ortho-Profile method are 11 human cytochrome c oxidase (COX) assembly proteins that are implicated in mitochondrial function and disease. Their co-expression patterns, experimentally verified subcellular localization, and co-purification with human COX-associated proteins support these predictions. For the human gene C12orf62, the ortholog of S. cerevisiae COX14, we specifically confirm its role in negative regulation of the translation of cytochrome c oxidase.ConclusionsDivergent homologs can often only be detected by comparing sequence profiles and profile-based hidden Markov models. The Ortho-Profile method takes advantage of these techniques in the quest for orthologs.

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MassNet: a functional annotation service for protein mass spectrometry data

Cited by 9 publications

References 28 publications

Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles

Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles

PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440

Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase

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