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- Berglund, Ann-Charlotte, et al.
(författare)
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InParanoid 6 : eukaryotic ortholog clusters with inparalogs
- 2008
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 36, s. D263-D266
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Tidskriftsartikel (refereegranskat)abstract
- The InParanoid eukaryotic ortholog database (http://InParanoid.sbc.su.se/) has been updated to version 6 and is now based on 35 species. We collected all available 'complete' eukaryotic proteomes and Escherichia coli, and calculated ortholog groups for all 595 species pairs using the InParanoid program. This resulted in 2 642 187 pairwise ortholog groups in total. The orthology-based species relations are presented in an orthophylogram. InParanoid clusters contain one or more orthologs from each of the two species. Multiple orthologs in the same species, i.e. inparalogs, result from gene duplications after the species divergence. A new InParanoid website has been developed which is optimized for speed both for users and for updating the system. The XML output format has been improved for efficient processing of the InParanoid ortholog clusters.
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| 4. |
- Lindahl, Bertil, 1957-, et al.
(författare)
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Poor long-term prognosis in patients admitted with strong suspicion of acute myocardial infarction but discharged with another diagnosis
- 2021
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Ingår i: Journal of Internal Medicine. - : Wiley. - 0954-6820 .- 1365-2796. ; 290:2, s. 359-372
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Tidskriftsartikel (refereegranskat)abstract
- Background: Characteristics and prognosis of patients admitted with strong suspicion of myocardial infarction (MI) but discharged without an MI diagnosis are not well-described. Objectives: To compare background characteristics and cardiovascular outcomes in patients discharged with or without MI diagnosis. Methods: The DETermination of the role of Oxygen in suspected Acute Myocardial Infarction (DETO2X-AMI) trial compared 6629 patients with strong suspicion of MI randomized to oxygen or ambient air. The main composite end-point of this subgroup analysis was the incidence of all-cause death, rehospitalization with MI, heart failure (HF) or stroke during a follow-up of 2.1 years (median; range: 1–3.7 years) irrespective of randomized treatment. Results: 1619 (24%) received a non-MI discharge diagnosis, and 5010 patients (76%) were diagnosed with MI. Groups were similar in age, but non-MI patients were more commonly female and had more comorbidities. At thirty days, the incidence of the composite end-point was 2.8% (45 of 1619) in non-MI patients, compared to 5.0% (250 of 5010) in MI patients with lower incidences in all individual end-points. However, for the long-term follow-up, the incidence of the composite end-point increased in the non-MI patients to 17.7% (286 of 1619) as compared to 16.0% (804 of 5010) in MI patients, mainly driven by a higher incidence of all-cause death, stroke and HF. Conclusions: Patients admitted with a strong suspicion of MI but discharged with another diagnosis had more favourable outcomes in the short-term perspective, but from one year onwards, cardiovascular outcomes and death deteriorated to a worse long-term prognosis.
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| 7. |
- Sonnhammer, Erik L. L., et al.
(författare)
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InParanoid 8 : orthology analysis between 273 proteomes, mostly eukaryotic
- 2015
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 43:D1, s. D234-D239
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Tidskriftsartikel (refereegranskat)abstract
- The InParanoid database (http://InParanoid.sbc.su.se) provides a user interface to orthologs inferred by the InParanoid algorithm. As there are now international efforts to curate and standardize complete proteomes, we have switched to using these resources rather than gathering and curating the proteomes ourselves. InParanoid release 8 is based on the 66 reference proteomes that the 'Quest for Orthologs' community has agreed on using, plus 207 additional proteomes from the UniProt complete proteomes-in total 273 species. These represent 246 eukaryotes, 20 bacteria and seven archaea. Compared to the previous release, this increases the number of species by 173% and the number of pairwise species comparisons by 650%. In turn, the number of ortholog groups has increased by 423%. We present the contents and usages of InParanoid 8, and a detailed analysis of how the proteome content has changed since the previous release.
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| 8. |
- Östlund, Gabriel, et al.
(författare)
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Avoiding pitfalls in gene (co)expression meta-analysis
- 2014
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Ingår i: Genomics. - : Elsevier BV. - 0888-7543 .- 1089-8646. ; 103:1, s. 21-30
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Tidskriftsartikel (refereegranskat)abstract
- Differential gene expression analysis between healthy and diseased groups is a widely used approach to understand the molecular underpinnings of disease. A wide variety of experimental and bioinformatics techniques are available for this type of analysis, yet their impact on the reliability of the results has not been systematically studied. We performed a large scale comparative analysis of clinical expression data, using several background corrections and differential expression metrics. The agreement between studies was analyzed for study pairs of same cancer type, of different cancer types, and between cancer and non-cancer studies. We also replicated the analysis using differential coexpression. We found that agreement of differential expression is primarily dictated by the microarray platform, while differential coexpression requires large sample sizes. Two studies using different differential expression metrics may show no agreement, even if they agree strongly using the same metric. Our analysis provides practical recommendations for gene (co)expression analysis.
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| 9. |
- Östlund, Gabriel, 1980-, et al.
(författare)
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InParanoid 7 : new algorithms and tools for eukaryotic orthology analysis
- 2010
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 38:1, s. D196-D203
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Tidskriftsartikel (refereegranskat)abstract
- The InParanoid project gathers proteomes of completely sequenced eukaryotic species plus Escherichia coli and calculates pairwise ortholog relationships among them. The new release 7.0 of the database has grown by an order of magnitude over the previous version and now includes 100 species and their collective 1.3 million proteins organized into 42.7 million pairwise ortholog groups. The InParanoid algorithm itself has been revised and is now both more specific and sensitive. Based on results from our recent benchmarking of low-complexity filters in homology assignment, a two-pass BLAST approach was developed that makes use of high-precision compositional score matrix adjustment, but avoids the alignment truncation that sometimes follows. We have also updated the InParanoid web site (http://InParanoid.sbc.su.se). Several features have been added, the response times have been improved and the site now sports a new, clearer look. As the number of ortholog databases has grown, it has become difficult to compare among these resources due to a lack of standardized source data and incompatible representations of ortholog relationships. To facilitate data exchange and comparisons among ortholog databases, we have developed and are making available two XML schemas: SeqXML for the input sequences and OrthoXML for the output ortholog clusters.
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| 10. |
- Östlund, Gabriel, 1980-, et al.
(författare)
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Network-based Identification of Novel Cancer Genes
- 2010
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Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 9:4, s. 648-655
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Tidskriftsartikel (refereegranskat)abstract
- Genes involved in cancer susceptibility and progression can serve as templates for searching protein networks for novel cancer genes. To this end, we introduce a general network searching method, MaxLink, and apply it to find and rank cancer gene candidates by their connectivity to known cancer genes. Using a comprehensive protein interaction network, we searched for genes connected to known cancer genes. First, we compiled a new set of 812 genes involved in cancer, more than twice the number in the Cancer Gene Census. Their network neighbors were then extracted. This candidate list was refined by selecting genes with unexpectedly high levels of connectivity to cancer genes and without previous association to cancer. This produced a list of 1891 new cancer candidates with up to 55 connections to known cancer genes. We validated our method by cross-validation, Gene Ontology term bias, and differential expression in cancer versus normal tissue. An example novel cancer gene candidate is presented with detailed analysis of the local network and neighbor annotation. Our study provides a ranked list of high priority targets for further studies in cancer research. Supplemental material is included.
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