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Asoke K. Talukder Shashidhar Ravishankar Krittika Sasmal Santhosh Gandham Jyothsna Prabhukumar Prahalad H. Achutharao Debmalya Barh Francesco Blasi 《PloS one》2015,10(4)
In translational cancer medicine, implicated pathways and the relevant master genes are of focus. Exome''s specificity, processing-time, and cost advantage makes it a compelling tool for this purpose. However, analysis of exome lacks reliable combinatory analysis tools and techniques. In this paper we present XomAnnotate – a meta- and functional-analysis software for exome. We compared UnifiedGenotyper, Freebayes, Delly, and Lumpy algorithms that were designed for whole-genome and combined their strengths in XomAnnotate for exome data through meta-analysis to identify comprehensive mutation profile (SNPs/SNVs, short inserts/deletes, and SVs) of patients. The mutation profile is annotated followed by functional analysis through pathway enrichment and network analysis to identify most critical genes and pathways implicated in the disease genesis. The efficacy of the software is verified through MDS and clustering and tested with available 11 familial non-BRCA1/BRCA2 breast cancer exome data. The results showed that the most significantly affected pathways across all samples are cell communication and antigen processing and presentation. ESCO1, HYAL1, RAF1 and PRKCA emerged as the key genes. Network analysis further showed the purine and propanotate metabolism pathways along with RAF1 and PRKCA genes to be master regulators in these patients. Therefore, XomAnnotate is able to use exome data to identify entire mutation landscape, pathways, and the master genes accurately with wide concordance from earlier microarray and whole-genome studies -- making it a suitable biomedical software for using exome in next-generation translational medicine.
Availability
http://www.iomics.in/research/XomAnnotate 相似文献4.
Coelho-Rocha Nina Dias de Jesus Luís Cláudio Lima Barroso Fernanda Alvarenga Lima da Silva Tales Fernando Ferreira Enio Gonçalves José Eduardo dos Santos Martins Flaviano de Oliveira Carvalho Rodrigo Dias Barh Debmalya Azevedo Vasco Ariston de Carvalho 《Probiotics and antimicrobial proteins》2023,15(1):160-174
Probiotics and Antimicrobial Proteins - Beneficial effects of Lactiplantibacillus plantarum strains have been widely reported. Knowing that the effects of probiotic bacteria are strain-dependent,... 相似文献
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Rommel Thiago Jucá Ramos Adriana Ribeiro Carneiro Vasco Azevedo Maria Paula Schneider Debmalya Barh Artur Silva 《Bioinformation》2012,8(20):996-999
Modern genomic sequencing technologies produce a large amount of data with reduced cost per base; however, this data consists
of short reads. This reduction in the size of the reads, compared to those obtained with previous methodologies, presents new
challenges, including a need for efficient algorithms for the assembly of genomes from short reads and for resolving repetitions.
Additionally after abinitio assembly, curation of the hundreds or thousands of contigs generated by assemblers demands
considerable time and computational resources. We developed Simplifier, a stand-alone software that selectively eliminates
redundant sequences from the collection of contigs generated by ab initio assembly of genomes. Application of Simplifier to data
generated by assembly of the genome of Corynebacterium pseudotuberculosis strain 258 reduced the number of contigs generated by
ab initio methods from 8,004 to 5,272, a reduction of 34.14%; in addition, N50 increased from 1 kb to 1.5 kb. Processing the contigs of
Escherichia coli DH10B with Simplifier reduced the mate-paired library 17.47% and the fragment library 23.91%. Simplifier removed
redundant sequences from datasets produced by assemblers, thereby reducing the effort required for finalization of genome
assembly in tests with data from Prokaryotic organisms.
Availability
Simplifier is available at http://www.genoma.ufpa.br/rramos/softwares/simplifier.xhtmlIt requires Sun jdk 6 or higher. 相似文献6.
Loïc Baumann Joanna Vega Joris Philip Fabien Polese Fabrice Vétillard Maud Pierre Romaric Le Barh Philippe Jatteau Agnès Bardonnet Marie-Laure Acolas 《Journal of fish biology》2021,98(1):112-131
The ecology of the young stages of allis shad Alosa alosa is poorly documented, although they can be exposed to many pressures during their freshwater phase and their downstream migration. When passing through systems such as the Gironde-Garonne-Dordogne watershed (GGD, SW France), they can be subjected to high temperatures and low levels of oxygen (hypoxia). The aim of this work is to assess the tolerance of young Alosa alosa at four ages (c. 10, 30, 60 and 85 days old) by challenging them to different temperatures (18, 22, 26 and 28°C) together with decreasing oxygen saturation levels (from 100% to 30%). Survival of the 10-day-old individuals was not influenced by oxy-thermic conditions, but high stress levels were detected and perhaps this age class was too fragile regarding the constraint of the experimental design. Survival at 30 and at 60 days old was negatively influenced by the highest temperatures tested alone (from 26°C and from 28°C, respectively) but no effect was detected at 85 days old up to 28°C. A combined effect of temperature and oxygen level was highlighted, with heat accelerating survival decrease when associated with oxygen level depletion: essentially, survival was critical (<50%) at 30 days old at temperature ≥22°C together with 30% O2; at 60 days old, at temperature = 28°C with 30% O2; at 85 days old, at temperature ≥26°C with ≤40% O2. Tolerance to oxy-thermic pressures appeared to be greater among the migratory ages (60 and 85 days old) than among the 30-day-old group. Based on environmental data recorded in the GGD system and on our experimental results, an exploratory analysis allowed a discussion of the possible impact of past oxy-thermic conditions on the local population dynamics between 2005 and 2018. The oxy-thermic conditions that may affect Alosa alosa at ages when they migrate downstream (60 and 85 days old) were not frequently recorded in this period, except in cases of extreme episodes of heat together with hypoxia that occurred in some years, in summertime in the turbidity maximum zone of the Gironde estuary (particularly in the year 2006). Interestingly, oxy-thermic conditions that are likely to threaten the 30-day-old individuals occurred more frequently in the lower freshwater parts of the GGD system between the years 2005 and 2018. In the context of climate change, a general increase in temperature is predicted, as well as more frequent and severe hypoxic events, therefore we suggest that local Alosa alosa population recruitment could encounter critical oxy-thermic conditions more frequently in the future if no adaptive management of water resources occurs. 相似文献
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Aristóteles Góes-Neto Olga Kukharenko Iryna Orlovska Olga Podolich Madangchanok Imchen Ranjith Kumavath Rodrigo Bentes Kato Daniel Santana de Carvalho Sandeep Tiwari Bertram Brenig Vasco Azevedo Oleg Reva Jean-Pierre P. de Vera Natalia Kozyrovska Debmalya Barh 《Environmental microbiology》2021,23(7):3727-3742
Kombucha is a multispecies microbial ecosystem mainly composed of acetic acid bacteria and osmophilic acid-tolerant yeasts, which is used to produce a probiotic drink. Furthermore, Kombucha Mutualistic Community (KMC) has been recently proposed to be used during long space missions as both a living functional fermented product to improve astronauts' health and an efficient source of bacterial nanocellulose. In this study, we compared KMC structure and functions before and after samples were exposed to the space/Mars-like environment outside the International Space Station in order to investigate the changes related to their re-adaptation to Earth-like conditions by shotgun metagenomics, using both diversity and functional analyses of Community Ecology and Complex Networks approach. Our study revealed that the long-term exposure to space/Mars-like conditions on low Earth orbit may disorganize the KMC to such extent that it will not restore the initial community structure; however, KMC core microorganisms of the community were maintained. Nonetheless, there were no significant differences in the community functions, meaning that the KMC communities are ecologically resilient. Therefore, despite the extremely harsh conditions, key KMC species revived and provided the community with the genetic background needed to survive long periods of time under extraterrestrial conditions. 相似文献
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Cerdeira LT Schneider MP Pinto AC de Almeida SS dos Santos AR Barbosa EG Ali A Aburjaile FF de Abreu VA Guimarães LC Soares Sde C Dorella FA Rocha FS Bol E Gomes de Sá PH Lopes TS Barbosa MS Carneiro AR Jucá Ramos RT Coimbra NA Lima AR Barh D Jain N Tiwari S Raja R Zambare V Ghosh P Trost E Tauch A Miyoshi A Azevedo V Silva A 《Journal of bacteriology》2011,193(24):7025-7026
In this work, we report the whole-genome sequence of Corynebacterium pseudotuberculosis bv. equi strain CIP 52.97 (Collection Institut Pasteur), isolated in 1952 from a case of ulcerative lymphangitis in a Kenyan horse, which has evidently caused significant losses to agribusiness. Therefore, obtaining this genome will allow the detection of important targets for postgenomic studies, with the aim of minimizing problems caused by this microorganism. 相似文献
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Pratap Devarapalli Ranjith N Kumavath Debmalya Barh Vasco Azevedo 《Bioinformation》2014,10(9):586-591
Turritopsis nutricula (T. nutricula) is the one of the known reported organisms that can revert its life cycle to the polyp stage evenafter becoming sexually mature, defining itself as the only immortal organism in the animal kingdom. Therefore, the animal ishaving prime importance in basic biological, aging, and biomedical researches. However, till date, the genome of this organism hasnot been sequenced and even there is no molecular phylogenetic study to reveal its close relatives. Here, using phylogeneticanalysis based on available 16s rRNA gene and protein sequences of Cytochrome oxidase subunit-I (COI or COX1) of T. nutricula,we have predicted the closest relatives of the organism. While we found Nemopsis bachei could be closest organism based on COX1gene sequence; T. dohrnii may be designated as the closest taxon to T. nutricula based on rRNA. Moreover, we have figured out fourspecies that showed similar root distance based on COX1 protein sequence. 相似文献