ACTuDB, a new database for the integrated analysis of array-CGH and clinical data for tumors

Hupé, Philippe; Rosa, Philippe La; Liva, Stéphane; Lair, Séverine; Servant, Nicolas; Barillot, Emmanuel

doi:10.1038/sj.onc.1210488

Cited by 11 publications

(7 citation statements)

References 34 publications

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“…The Visualization and Analysis of array-CGH, transcriptome and other Molecular Profiles (VAMP) (13) resource was employed for microarray-CGH data analysis of chromosome region 7q11.23 from MCF7, T47D and ZR75 breast cancer cell lines. In silico analysis of Pollack’s data (14) identified a gain of chromosome region 7q11.22 - 7q11.23 including the RHBDD2 gene region in MCF7 and T47D cell lines (Fig. 5A).…”

Section: Resultsmentioning

confidence: 99%

“…VAMP is a graphical user interface for visualization and analysis of genomic profiles (13). The chromosome 7 array-CGH profiles previously generated by Pollack et al (12) from MCF7, T47D and ZR75 breast cancer cell lines were download from the ACTuDB database at the same website (14). The frequency of DNA gains/losses affecting the chromosome region 7q11.23 was determined from a cumulative set of 552 IDC analyzed by array-CGH based on a publicly available Progenetix database (http://www.progenetix.net) (9).…”

Section: Methodsmentioning

confidence: 99%

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Rhomboid domain containing 2 (RHBDD2): A novel cancer-related gene over-expressed in breast cancer

Abba

Lacunza

Nunez

et al. 2009

Biochimica et Biophysica Acta (BBA) - Molecular Basis of Diseas

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In the course of breast cancer global gene expression studies, we identified an uncharacterized gene known as RHBDD2 (Rhomboid domain containing 2) to be markedly over-expressed in primary tumors from patients with recurrent disease. In this study, we identified RHBDD2 mRNA and protein expression significantly elevated in breast carcinomas compared with normal breast samples as analyzed by SAGE (n=46) and immunohistochemistry (n=213). Interestingly, specimens displaying RHBDD2 over-expression were predominantly advanced stage III breast carcinomas (p=0.001). Western-blot, RT-PCR and cDNA sequencing analyses allowed us to identify two RHBDD2 alternatively spliced mRNA isoforms expressed in breast cancer cell lines. We further investigated the occurrence and frequency of gene amplification and over-expression affecting RHBDD2 in 131 breast samples. RHBDD2 gene amplification was detected in 21% of 98 invasive breast carcinomas analyzed. However, no RHBDD2 amplification was detected in normal breast tissues (n=17) or breast benign lesions (n=16) (p=0.014). Interestingly, siRNA mediated silencing of RHBDD2 expression results in a decrease of MCF7 breast cancer cells proliferation compared with the corresponding controls (p=0.001). In addition, analysis of publicly available gene expression data showed a strong association between high RHBDD2 expression and decreased overall survival (p=0.0023), relapse-free survival (p= 0.0013), and metastasis-free interval (p=0.006) in patients with primary ER-negative breast carcinomas. In conclusion, our findings suggest that RHBDD2 over-expression behaves as an indicator of poor prognosis and may play a role facilitating breast cancer progression.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Rhomboid domain containing 2 (RHBDD2): A novel cancer-related gene over-expressed in breast cancer

Abba

Lacunza

Nunez

et al. 2009

Biochimica et Biophysica Acta (BBA) - Molecular Basis of Diseas

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“…Majority have a focus on genomics rather than a proteomics approach unlike RASOnD which provides detailed information on both aspects. These databases include ACTuDB [41], Catalog of Somatic Mutations in Cancer (COSMIC) database [42], Dragon database for exploration of ovarian cancer genes (DDOC) [43], kinase pathway database [44], mouse genome database [45], Oncogenomic Database of Hepatocellular carcinoma (OncoDB.HCC) [46], rat genome database (RGD) [47], Signal Transduction Classification (STCDB) [48], Tumor gene family of databases (TGDB) [49] and Genecards [50]. The rat and mouse genome databases are useful if the focus of search is on these species.…”

Section: Discussionmentioning

confidence: 99%

RASOnD - A comprehensive resource and search tool for RAS superfamily oncogenes from various species

et al. 2011

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BackgroundThe Ras superfamily plays an important role in the control of cell signalling and division. Mutations in the Ras genes convert them into active oncogenes. The Ras oncogenes form a major thrust of global cancer research as they are involved in the development and progression of tumors. This has resulted in the exponential growth of data on Ras superfamily across different public databases and in literature. However, no dedicated public resource is currently available for data mining and analysis on this family. The present database was developed to facilitate straightforward accession, retrieval and analysis of information available on Ras oncogenes from one particular site.DescriptionWe have developed the RAS Oncogene Database (RASOnD) as a comprehensive knowledgebase that provides integrated and curated information on a single platform for oncogenes of Ras superfamily. RASOnD encompasses exhaustive genomics and proteomics data existing across diverse publicly accessible databases. This resource presently includes overall 199,046 entries from 101 different species. It provides a search tool to generate information about their nucleotide and amino acid sequences, single nucleotide polymorphisms, chromosome positions, orthologies, motifs, structures, related pathways and associated diseases. We have implemented a number of user-friendly search interfaces and sequence analysis tools. At present the user can (i) browse the data (ii) search any field through a simple or advance search interface and (iii) perform a BLAST search and subsequently CLUSTALW multiple sequence alignment by selecting sequences of Ras oncogenes. The Generic gene browser, GBrowse, JMOL for structural visualization and TREEVIEW for phylograms have been integrated for clear perception of retrieved data. External links to related databases have been included in RASOnD.ConclusionsThis database is a resource and search tool dedicated to Ras oncogenes. It has utility to cancer biologists and cell molecular biologists as it is a ready source for research, identification and elucidation of the role of these oncogenes. The data generated can be used for understanding the relationship between the Ras oncogenes and their association with cancer. The database updated monthly is freely accessible online at http://202.141.47.181/rasond/ and http://www.aiims.edu/RAS.html.

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“…Examples include the GLAD and CBS algorithms [23,24]. Genotyping arrays provide an additional useful metric, the allelic ratio, which can be utilized for assessing the copy number state of each segment.…”

Section: Methodsmentioning

confidence: 99%

CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics

et al. 2010

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BackgroundRecent studies have shown that copy number variations (CNVs) are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly assessing research and clinical samples for CNV content, as well as for determining the potential pathogenicity of identified variants. However, few informatics tools for accurate and efficient CNV detection and assessment currently exist.ResultsWe developed a suite of software tools and resources (CNV Workshop) for automated, genome-wide CNV detection from a variety of SNP array platforms. CNV Workshop includes three major components: detection, annotation, and presentation of structural variants from genome array data. CNV detection utilizes a robust and genotype-specific extension of the Circular Binary Segmentation algorithm, and the use of additional detection algorithms is supported. Predicted CNVs are captured in a MySQL database that supports cohort-based projects and incorporates a secure user authentication layer and user/admin roles. To assist with determination of pathogenicity, detected CNVs are also annotated automatically for gene content, known disease loci, and gene-based literature references. Results are easily queried, sorted, filtered, and visualized via a web-based presentation layer that includes a GBrowse-based graphical representation of CNV content and relevant public data, integration with the UCSC Genome Browser, and tabular displays of genomic attributes for each CNV.ConclusionsTo our knowledge, CNV Workshop represents the first cohesive and convenient platform for detection, annotation, and assessment of the biological and clinical significance of structural variants. CNV Workshop has been successfully utilized for assessment of genomic variation in healthy individuals and disease cohorts and is an ideal platform for coordinating multiple associated projects.Availability and ImplementationAvailable on the web at: http://sourceforge.net/projects/cnv

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ACTuDB, a new database for the integrated analysis of array-CGH and clinical data for tumors

Cited by 11 publications

References 34 publications

Rhomboid domain containing 2 (RHBDD2): A novel cancer-related gene over-expressed in breast cancer

Rhomboid domain containing 2 (RHBDD2): A novel cancer-related gene over-expressed in breast cancer

RASOnD - A comprehensive resource and search tool for RAS superfamily oncogenes from various species

CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics

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