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971.
Background
The analysis of high-throughput data in biology is aided by integrative approaches such as gene-set analysis. Gene-sets can represent well-defined biological entities (e.g. metabolites) that interact in networks (e.g. metabolic networks), to exert their function within the cell. Data interpretation can benefit from incorporating the underlying network, but there are currently no optimal methods that link gene-set analysis and network structures.Results
Here we present Kiwi, a new tool that processes output data from gene-set analysis and integrates them with a network structure such that the inherent connectivity between gene-sets, i.e. not simply the gene overlap, becomes apparent. In two case studies, we demonstrate that standard gene-set analysis points at metabolites regulated in the interrogated condition. Nevertheless, only the integration of the interactions between these metabolites provides an extra layer of information that highlights how they are tightly connected in the metabolic network.Conclusions
Kiwi is a tool that enhances interpretability of high-throughput data. It allows the users not only to discover a list of significant entities or processes as in gene-set analysis, but also to visualize whether these entities or processes are isolated or connected by means of their biological interaction. Kiwi is available as a Python package at http://www.sysbio.se/kiwi and an online tool in the BioMet Toolbox at http://www.biomet-toolbox.org.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-014-0408-9) contains supplementary material, which is available to authorized users. 相似文献972.
Lapidus A Clum A Labutti K Kaluzhnaya MG Lim S Beck DA Glavina Del Rio T Nolan M Mavromatis K Huntemann M Lucas S Lidstrom ME Ivanova N Chistoserdova L 《Journal of bacteriology》2011,193(15):3757-3764
The genomes of three representatives of the family Methylophilaceae, Methylotenera mobilis JLW8, Methylotenera versatilis 301, and Methylovorus glucosetrophus SIP3-4, all isolated from a single study site, Lake Washington in Seattle, WA, were completely sequenced. These were compared to each other and to the previously published genomes of Methylobacillus flagellatus KT and an unclassified Methylophilales strain, HTCC2181. Comparative analysis revealed that the core genome of Methylophilaceae may be as small as approximately 600 genes, while the pangenome may be as large as approximately 6,000 genes. Significant divergence between the genomes in terms of both gene content and gene and protein conservation was uncovered, including the varied presence of certain genes involved in methylotrophy. Overall, our data demonstrate that metabolic potentials can vary significantly between different species of Methylophilaceae, including organisms inhabiting the very same environment. These data suggest that genetic divergence among the members of this family may be responsible for their specialized and nonredundant functions in C? cycling, which in turn suggests means for their successful coexistence in their specific ecological niches. 相似文献
973.
Svenning MM Hestnes AG Wartiainen I Stein LY Klotz MG Kalyuzhnaya MG Spang A Bringel F Vuilleumier S Lajus A Médigue C Bruce DC Cheng JF Goodwin L Ivanova N Han J Han CS Hauser L Held B Land ML Lapidus A Lucas S Nolan M Pitluck S Woyke T 《Journal of bacteriology》2011,193(22):6418-6419
Methylobacter tundripaludum SV96T (ATCC BAA-1195) is a psychrotolerant aerobic methane-oxidizing gammaproteobacterium (Methylococcales, Methylococcaceae) living in High Arctic wetland soil. The strain was isolated from soil harvested in July 1996 close to the settlement Ny-Ålesund, Svalbard, Norway (78°56′N, 11°53′E), and described as a novel species in 2006. The genome includes pmo and pxm operons encoding copper membrane monooxygenases (Cu-MMOs), genes required for nitrogen fixation, and the nirS gene implicated in dissimilatory nitrite reduction to NO but no identifiable inventory for further processing of nitrogen oxides. These genome data provide the basis to investigate M. tundripaludum SV96, identified as a major player in the biogeochemistry of Arctic environments. 相似文献
974.
Sales CM Mahendra S Grostern A Parales RE Goodwin LA Woyke T Nolan M Lapidus A Chertkov O Ovchinnikova G Sczyrba A Alvarez-Cohen L 《Journal of bacteriology》2011,193(17):4549-4550
Pseudonocardia dioxanivorans CB1190 is the first bacterium reported to be capable of growth on the environmental contaminant 1,4-dioxane and the first member of the genus Pseudonocardia for which there is an annotated genome sequence. Preliminary analysis of the genome (chromosome and three plasmids) indicates that strain CB1190 possesses several multicomponent monooxygenases that could be involved in the aerobic degradation of 1,4-dioxane and other environmental contaminants. 相似文献
975.
Blumer-Schuette SE Ozdemir I Mistry D Lucas S Lapidus A Cheng JF Goodwin LA Pitluck S Land ML Hauser LJ Woyke T Mikhailova N Pati A Kyrpides NC Ivanova N Detter JC Walston-Davenport K Han S Adams MW Kelly RM 《Journal of bacteriology》2011,193(6):1483-1484
The genus Caldicellulosiruptor contains the most thermophilic, plant biomass-degrading bacteria isolated to date. Previously, genome sequences from three cellulolytic members of this genus were reported (C. saccharolyticus, C. bescii, and C. obsidiansis). To further explore the physiological and biochemical basis for polysaccharide degradation within this genus, five additional genomes were sequenced: C. hydrothermalis, C. kristjanssonii, C. kronotskyensis, C. lactoaceticus, and C. owensensis. Taken together, the seven completed and one draft-phase Caldicellulosiruptor genomes suggest that, while central metabolism is highly conserved, significant differences in glycoside hydrolase inventories and numbers of carbohydrate transporters exist, a finding which likely relates to variability observed in plant biomass degradation capacity. 相似文献
976.
Recent results show that treatments with reducing agents, including the sulfur oxyanions dithionite and hydrogen sulfite, efficiently improve the fermentability of inhibitory lignocellulose hydrolysates, and that the treatments are effective when the reducing agents are added in situ into the fermentation vessel at low temperature. In the present investigation, dithionite was added to medium with model inhibitors (coniferyl aldehyde, furfural, 5-hydroxymethylfurfural, or acetic acid) and the effects on the fermentability with yeast were studied. Addition of 10 mM dithionite to medium containing 2.5 mM coniferyl aldehyde resulted in a nine-fold increase in the glucose consumption rate and a three-fold increase in the ethanol yield. To investigate the mechanism behind the positive effects of adding sulfur oxyanions, mixtures containing 2.5 mM of a model inhibitor (an aromatic compound, a furan aldehyde, or an aliphatic acid) and 15 mM dithionite or hydrogen sulfite were analyzed using mass spectrometry (MS). The results of the analyses, which were performed by using UHPLC-ESI-TOF-MS and UHPLC-LTQ/Orbitrap-MS/MS, indicate that the positive effects of sulfur oxyanions are primarily due to their capability to react with and sulfonate inhibitory aromatic compounds and furan aldehydes at low temperature and slightly acidic pH (such as 25°C and pH 5.5). 相似文献
977.
van Passel MW Kant R Palva A Copeland A Lucas S Lapidus A Glavina del Rio T Pitluck S Goltsman E Clum A Sun H Schmutz J Larimer FW Land ML Hauser L Kyrpides N Mikhailova N Richardson PP Janssen PH de Vos WM Smidt H 《Journal of bacteriology》2011,193(9):2367-2368
Bacteria of the deeply branching phylum Verrucomicrobia are rarely cultured yet commonly detected in metagenomic libraries from aquatic, terrestrial, and intestinal environments. We have sequenced the genome of Opitutus terrae PB90-1, a fermentative anaerobe within this phylum, isolated from rice paddy soil and capable of propionate production from plant-derived polysaccharides. 相似文献
978.
Coleman NV Wilson NL Barry K Brettin TS Bruce DC Copeland A Dalin E Detter JC Del Rio TG Goodwin LA Hammon NM Han S Hauser LJ Israni S Kim E Kyrpides N Land ML Lapidus A Larimer FW Lucas S Pitluck S Richardson P Schmutz J Tapia R Thompson S Tice HN Spain JC Gossett JG Mattes TE 《Journal of bacteriology》2011,193(13):3399-3400
Nocardioides sp. strain JS614 grows on ethene and vinyl chloride (VC) as sole carbon and energy sources and is of interest for bioremediation and biocatalysis. Sequencing of the complete genome of JS614 provides insight into the genetic basis of alkene oxidation, supports ongoing research into the physiology and biochemistry of growth on ethene and VC, and provides biomarkers to facilitate detection of VC/ethene oxidizers in the environment. This is the first genome sequence from the genus Nocardioides and the first genome of a VC/ethene-oxidizing bacterium. 相似文献
979.
Vishnivetskaya TA Lucas S Copeland A Lapidus A Glavina del Rio T Dalin E Tice H Bruce DC Goodwin LA Pitluck S Saunders E Brettin T Detter C Han C Larimer F Land ML Hauser LJ Kyrpides NC Ovchinnikova G Kathariou S Ramaley RF Rodrigues DF Hendrix C Richardson P Tiedje JM 《Journal of bacteriology》2011,193(11):2880-2881
Here we present the genome of strain Exiguobacterium sp. AT1b, a thermophilic member of the genus Exiguobacterium whose representatives were isolated from various environments along a thermal and physicochemical gradient. This genome was sequenced to be a comparative resource for the study of thermal adaptation with a psychroactive representative of the genus, Exiguobacterium sibiricum strain 255-15, that was previously sequenced by the U.S. Department of Energy's (DOE's) Joint Genome Institute (JGI) (http://genome.ornl.gov/microbial/exig/). 相似文献
980.
van Passel MW Kant R Palva A Lucas S Copeland A Lapidus A Glavina del Rio T Dalin E Tice H Bruce D Goodwin L Pitluck S Davenport KW Sims D Brettin TS Detter JC Han S Larimer FW Land ML Hauser L Kyrpides N Ovchinnikova G Richardson PP de Vos WM Smidt H Zoetendal EG 《Journal of bacteriology》2011,193(9):2373-2374
Victivallis vadensis ATCC BAA-548 represents the first cultured representative from the novel phylum Lentisphaerae, a deep-branching bacterial lineage. Few cultured bacteria from this phylum are known, and V. vadensis therefore represents an important organism for evolutionary studies. V. vadensis is a strictly anaerobic sugar-fermenting isolate from the human gastrointestinal tract. 相似文献