AVATAR: A database for genome-wide alternative splicing event detection through analysis of large scale ESTs and mRNAs

Hsu, Fang‐Rong; Chang, Hwan‐You; Lin, Yaw-Lin; Tsai, Yin-Te; Peng, Hui-Ling; Chen, Ying-Tsong; Cheng, Chia Yang; Shih, Min Yao; Liu, Chia-Hung; Chen, Chin-Feng

doi:10.6026/97320630001016

Cited by 12 publications

(3 citation statements)

References 3 publications

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“…PALS db [105] provides the putative alternative splicing database based on UniGene clusters of human and mouse sources which mainly consist of EST data. Similarly, some databases such as EASED [107] and AVATAR [108] are constructed by datasets of EST and mRNAs. ASAP [106] provides the detail annotation for exon-intron boundary, alternative splicing, and its tissue specificity for the user to design probes for distinguishing different splicing isoforms.…”

Section: Alternative Splicing-related Bioinformatics Resourcesmentioning

confidence: 99%

Alternative Splicing for Diseases, Cancers, Drugs, and Databases

Tang

Lee

Hou

et al. 2013

The Scientific World Journal

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Alternative splicing is a major diversification mechanism in the human transcriptome and proteome. Several diseases, including cancers, have been associated with dysregulation of alternative splicing. Thus, correcting alternative splicing may restore normal cell physiology in patients with these diseases. This paper summarizes several alternative splicing-related diseases, including cancers and their target genes. Since new cancer drugs often target spliceosomes, several clinical drugs and natural products or their synthesized derivatives were analyzed to determine their effects on alternative splicing. Other agents known to have modulating effects on alternative splicing during therapeutic treatment of cancer are also discussed. Several commonly used bioinformatics resources are also summarized.

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Section: Alternative Splicing-related Bioinformatics Resourcesmentioning

confidence: 99%

Alternative Splicing for Diseases, Cancers, Drugs, and Databases

Tang

Lee

Hou

et al. 2013

The Scientific World Journal

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“…Sequence and microarray-based approaches have been used for defining the AS repertoire of human cells. The former includes several computational analyses concerning genomic and transcriptome alignments of human ESTs (expressed sequence tags) and mRNA databases [ 11 , 15 - 17 ] and cross-species alignment from closely related organisms [ 18 , 19 ]; the latter includes genomic and exon-intron junction microarray platforms [ 20 - 23 ]. Both approaches have contributed to the investigation of the expression pattern of AS variants and also facilitated the identification of novel AS variants.…”

Section: Introductionmentioning

confidence: 99%

Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts

Ferreira

Rangel

Galante³

et al. 2010

BMC Genomics

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BackgroundAlternative splicing (AS) is a central mechanism in the generation of genomic complexity and is a major contributor to transcriptome and proteome diversity. Alterations of the splicing process can lead to deregulation of crucial cellular processes and have been associated with a large spectrum of human diseases. Cancer-associated transcripts are potential molecular markers and may contribute to the development of more accurate diagnostic and prognostic methods and also serve as therapeutic targets. Alternative splicing-enriched cDNA libraries have been used to explore the variability generated by alternative splicing. In this study, by combining the use of trapping heteroduplexes and RNA amplification, we developed a powerful approach that enables transcriptome-wide exploration of the AS repertoire for identifying AS variants associated with breast tumor cells modulated by ERBB2 (HER-2/neu) oncogene expression.ResultsThe human breast cell line (C5.2) and a pool of 5 ERBB2 over-expressing breast tumor samples were used independently for the construction of two AS-enriched libraries. In total, 2,048 partial cDNA sequences were obtained, revealing 214 alternative splicing sequence-enriched tags (ASSETs). A subset with 79 multiple exon ASSETs was compared to public databases and reported 138 different AS events. A high success rate of RT-PCR validation (94.5%) was obtained, and 2 novel AS events were identified. The influence of ERBB2-mediated expression on AS regulation was evaluated by capillary electrophoresis and probe-ligation approaches in two mammary cell lines (Hb4a and C5.2) expressing different levels of ERBB2. The relative expression balance between AS variants from 3 genes was differentially modulated by ERBB2 in this model system.ConclusionsIn this study, we presented a method for exploring AS from any RNA source in a transcriptome-wide format, which can be directly easily adapted to next generation sequencers. We identified AS transcripts that were differently modulated by ERBB2-mediated expression and that can be tested as molecular markers for breast cancer. Such a methodology will be useful for completely deciphering the cancer cell transcriptome diversity resulting from AS and for finding more precise molecular markers.

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“…(FERREIRA et al, 2007). Além disso, apesar das predições computacionais necessitarem de confirmação experimental, elas podem identificar possíveis novas variantes, bem como sugerir a presença de elementos reguladores (CARTEGNI et al, 2003;HSU et al, 2005;SCHWARTZ;HALL;AST, 2009;SMITH et al, 2006). VENABLES, 2008b;GORLOV;SAUDERS, 2002).…”

Section: Figuraunclassified

Identificação de variantes de splicing sob influência da alta expressão do oncogene ERBB2 em câncer de mama

Ferreira¹

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AVATAR: A database for genome-wide alternative splicing event detection through analysis of large scale ESTs and mRNAs

Cited by 12 publications

References 3 publications

Alternative Splicing for Diseases, Cancers, Drugs, and Databases

Alternative Splicing for Diseases, Cancers, Drugs, and Databases

Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts

Identificação de variantes de splicing sob influência da alta expressão do oncogene ERBB2 em câncer de mama

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