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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2.
Thapa Lal B. Kaewchumnong Krittika Sinkkonen Aki Sridith Kitichate 《Plant Ecology》2020,221(10):883-892
Plant Ecology - Volatile compounds from leaf litter of invasive alien Ageratina adenophora are known to inhibit growth of native species in sub-tropical Asia, but there is not... 相似文献
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Manganese‐ and 1‐methyl‐4‐phenylpyridinium‐induced neurotoxicity display differences in morphological,electrophysiological and genome‐wide alterations: implications for idiopathic Parkinson's disease 下载免费PDF全文
Rajeswara Babu Mythri Narayana Reddy Raghunath Santosh Chandrakant Narwade Mirazkar Dasharatha Rao Pandareesh Kollarkandi Rajesh Sabitha Mohamad Aiyaz Bipin Chand Manas Sule Krittika Ghosh Senthil Kumar Bhagyalakshmi Shankarappa Soundarya Soundararajan Phalguni Anand Alladi Meera Purushottam Narayanappa Gayathri Deepti Dileep Deobagkar Thenkanidiyoor Rao Laxmi Muchukunte Mukunda Srinivas Bharath 《Journal of neurochemistry》2017,143(3):334-358
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Striga is a parasitic weed attacking mainly maize, sorghum, millet and cowpea. Studying the interaction between rice and Striga is valuable since rice is a model monocot. In this paper, the susceptibility of different rice cultivars to S. hermonthica was tested and quantitative trait loci (QTL) for Striga tolerance mapped on the Bala x Azucena F(6) population. Seven rice cultivars were grown with and without S. hermonthica for 14 wk. For the mapping experiment, 115 recombinant inbred lines (RILs), along with Azucena and Bala, were grown with and without Striga for 11 wk. Rice cultivars tested had different susceptibilities to Striga, ranging from highly susceptible to completely resistant. Azucena and Bala differed in the speed of Striga emergence and the impact on host growth. A genomic region between positions 139 and 166 cM on chromosome 1 was identified containing strong QTL (LOD = 4.9-15.7) for all traits measured. This indicates that genes for Striga tolerance exist in rice germplasm and the mapped QTL can be further studied to promote understanding of the nature of resistance/tolerance and breeding for Striga-resistant crop plants. 相似文献
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V. Guru KrishnaKumar Lokesh Baweja Krittika Ralhan Sharad Gupta 《Biochimica et Biophysica Acta (BBA)/General Subjects》2018,1862(12):2590-2604
Background
Carbamylation is a non-enzymatic post-translational modification (PTM), which involves the covalent modification of N-terminus of protein or ε-amino group of Lys. The role of carbamylation in several age-related disorders is well documented, however, the relationship between carbamylation and neurodegenerative disorders including Alzheimer's disease remains uncharted.Methods
In the present study, using aggregation-prone tau-core hexapeptide fragments 306VQIVYK311 (PHF6) and 275VQIINK280 (PHF6*) as models, we have elucidated the effect of carbamylation on aggregation kinetics and the changes occurring in the 3-dimensional architecture of fibrils using biophysical assays and molecular dynamics simulations.Results
We found that carbamylation aids in amyloid formation and can convert the unstructured off-pathway aggregates into robust amyloids, which were toxic to cells. Electron microscopy images and molecular dynamics simulations of PHF6 fibrils showed that carbamylated peptides can form excess hydrogen bonds and modulate the pitch length and twist of peptides fibrils. We have also compared N-terminal carbamylation to acetylation and further extended our finding to full length tau that exhibits aggregation upon carbamylation even in the absence of any external inducer.Conclusion
Our in vitro and in silico results together suggest that carbamylation can modulate the aggregation pathway of the amyloidegenic sequences and cause structural changes in fibril assemblies.General significance
Carbamylation acts as a switch, which triggers the aggregation in short amyloidogenic peptide fragments and modulate the structural changes in resulting amyloid fibrils. 相似文献6.
The LUminometric Methylation Assay (LUMA) measures global DNA methylation. LUMA depends on digestion of DNA with methyl‐sensitive and methyl‐insensitive restriction enzymes, followed by pyrosequencing. Until recently, LUMA has been principally used for biomedical research. Here, we use chickens as a model to investigate sample quality issues relating to LUMA and then apply the method to ecological species. First, we assessed the effect of tissue storage conditions on DNA methylation values. This is an important consideration for ecological species because samples are not always ideally preserved and LUMA is sensitive to poor DNA quality. We found that good quality LUMA data could be obtained from chicken liver and brain tissues stored at 21 °C for at least 2 and 12 h, respectively. Longer storage times introduced nonspecific peaks to pyrograms which were associated with reduced DNA methylation. Repeatedly, freezing and thawing the tissues did not affect LUMA data. Second, we measured DNA methylation in 12 species representing five animal classes: amphibians (African and Western clawed frog), reptiles (green anole lizard), fish (yellow perch, goldfish, lake trout), mammals (American mink, polar bear, short‐beaked common dolphin, Atlantic white‐sided dolphin) and birds (chicken, Japanese quail). We saw a pattern of high DNA methylation in fish (84–87%), and intermediate levels in mammals (68–72%) and birds (52–71%). This pattern corresponds well with previous measures of DNA methylation generated by HPLC. Our data represent the first CpG methylation values to be reported in several species and provide a basis for studying patterns of epigenetic inheritance in an ecological context. 相似文献
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