DBCAT: Database of CpG Islands and Analytical Tools for Identifying Comprehensive Methylation Profiles in Cancer Cells

Kuo, Hsien-Chi; Lin, Po‐Chun; Chung, Ting-Chiun; Chao, Chin-Mei; Lai, Liang‐Chuan; Tsai, Mong-Hsun; Chuang, Eric Y.

doi:10.1089/cmb.2010.0038

Cited by 38 publications

(15 citation statements)

References 10 publications

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“…18 The CpG islands have been located using the 'DataBase of CpG islands and Analytical Tool (DBCAT). 19 The DNA methylation possibilities have been studied using the epigenome browser, EpiGRAPH. 20 The various epigenetic factors have been analyzed using linear and non-linear kernels of 'Support Vector Machine (SVM) to compute the relevance of each attribute in making the predictions.…”

Section: Methodsmentioning

confidence: 99%

Evaluation of Colorectal Cancer (CRC) Epidemiology A Pharmacogenomic Approach

HimaVyshnavi¹,

C²,

Deepak³

et al. 2017

JYP

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Background: The population-wise variation in proneness of Colorectal Cancer (CRC) has been studied in the manuscript. A population wise analysis of responsiveness towards colorectal cancer is carried out with genetic, epigenetic, metagenomic and environmental factors associated with APC mutation mainly responsible for CRC among eight different populations. Methods and Material:The APC mutation has been obtained using the 'human gene mutation database-HGMD' and the 'international cancer genome consortium-ICGC' Data Portal. The epigenetic factors affecting colon cancer have been identified through EpiGRAPH tool. The 'human oral microbiome database (HOMD) and 'comparative toxicogenomics database (CTD)' are used to find the metagenomic factors affecting CRC. Results: Variants of APC gene from the selected ethnic classes chosen from Argentina,

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Section: Methodsmentioning

confidence: 99%

Evaluation of Colorectal Cancer (CRC) Epidemiology A Pharmacogenomic Approach

HimaVyshnavi¹,

C²,

Deepak³

et al. 2017

JYP

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“…In silico identification of CpG islands in target genes is based on common hits in different genome browsers (Ensembl, UCSC and NCBI) and online tools such as CpG Islands (The Sequence Manipulation Suite), DBCAT, Cpgplot (EMBOSS) and MethPrimer [19][20][21][22][23][24][25].…”

Section: ) In Silico Identification Of Cpg Islandsmentioning

confidence: 99%

An optimized strategy for cloning-based locus-specific bisulfite sequencing PCR

Poucke

Boulougouris

Spiegeleer

et al. 2017

Preprint

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In this methods paper, we describe a successful strategy to investigate locus-specific methylation by cloning-based bisulfite sequencing. We cover sample handling, DNA isolation, DNA quality control before bisulfite conversion, bisulfite conversion, DNA quality control after bisulfite conversion, in silico identification of CpG islands, methylation-independent bisulfite sequencing PCR (BSP) assay design, methylation-independent BSP, cloning strategy, sequencing and data analysis. Methods that are described nicely elsewhere will not be covered in detail. Instead, the focus will be on tips/tricks and new methods/strategies used in this protocol, including quality control assessment of the DNA before and after bisulfite conversion and a pooled cloning strategy to reduce time, costs and effort during this step. In addition we comment on dealing with bias and improving overall protocol efficiency.

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“…With the Sequence Manipulation Suite -CpG Islands Sequence Analysis option (Stothard, 2000), the occurrence of CpG islands was predicted. Also, with DBCAT (Kuo et al, 2011) the occurrence of CpG islands was investigated as well as the number of CpG per 1 kb within the mm, ll, bb and ss sequences.…”

Section: Global Dna Methylation Quantificationmentioning

confidence: 99%

Gene copy silencing and DNA methylation in natural and artificially produced allopolyploid fish

Matos

Coelho

Schartl

2016

Journal of Experimental Biology

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Allelic silencing is an important mechanism for coping with gene dosage changes in polyploid organisms that is well known in allopolyploid plants. Only recently, it was shown in the allotriploid fish Squalius alburnoides that this process also occurs in vertebrates. However, it is still unknown whether this silencing mechanism is common to other allopolyploid fish, and which mechanisms might be responsible for allelic silencing. We addressed these questions in a comparative study between Squalius alburnoides and another allopolyploid complex, the Amazon molly (Poecilia formosa). We examined the allelic expression patterns for three target genes in four somatic tissues of natural allo-anorthoploids and laboratory-produced trigenomic hybrids of S. alburnoides and P. formosa. Also, for both complexes, we evaluated the correlation between total DNA methylation level and the ploidy status and genomic composition of the individuals. We found that allelic silencing also occurs in other allopolyploid organisms besides the single one that was previously known. We found and discuss disparities within and between the two considered complexes concerning the pattern of allele-specific expression and DNA methylation levels. Disparities might be due to intrinsic characteristics of each genome involved in the hybridization process. Our findings also support the idea that long-term evolutionary processes have an effect on the allele expression patterns and possibly also on DNA methylation levels.

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DBCAT: Database of CpG Islands and Analytical Tools for Identifying Comprehensive Methylation Profiles in Cancer Cells

Cited by 38 publications

References 10 publications

Evaluation of Colorectal Cancer (CRC) Epidemiology A Pharmacogenomic Approach

Evaluation of Colorectal Cancer (CRC) Epidemiology A Pharmacogenomic Approach

An optimized strategy for cloning-based locus-specific bisulfite sequencing PCR

Gene copy silencing and DNA methylation in natural and artificially produced allopolyploid fish

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