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Genomic signatures characterize leukocyte infiltration in myositis muscles.

Wei Zhu | Katie Streicher | Nan Shen | Brandon W Higgs | Chris Morehouse | Lydia Greenlees | Anthony A Amato | Koustubh Ranade | Laura Richman | David Fiorentino | Bahija Jallal | Steven A Greenberg | Yihong Yao
BMC medical genomics | 2012

Leukocyte infiltration plays an important role in the pathogenesis and progression of myositis, and is highly associated with disease severity. Currently, there is a lack of: efficacious therapies for myositis; understanding of the molecular features important for disease pathogenesis; and potential molecular biomarkers for characterizing inflammatory myopathies to aid in clinical development.

Pubmed ID: 23171592

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R Project for Statistical Computing (tool)

RRID:SCR_001905

Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.

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Bioconductor (tool)

RRID:SCR_006442

Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.

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Broad Institute (tool)

RRID:SCR_007073

Biomedical and genomic research center located in Cambridge, Massachusetts, United States. Nonprofit research organization under the name Broad Institute Inc., and is partners with Massachusetts Institute of Technology, Harvard University, and the five Harvard teaching hospitals. Dedicated to advance understanding of biology and treatment of human disease to improve human health.

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Ingenuity Pathways Knowledge Base (tool)

RRID:SCR_008117

A horizontally and vertically structured database that pulls scientific and medical information and describes it consistently using the Ingenuity Ontology. The Knowledge Base pulls information from journals, public molecular content databases, and textbooks. Data is curated and and integrated into the Knowledge Base .

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PlantCyc (tool)

RRID:SCR_002110

Multi species reference database. Comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism.

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KEGG (tool)

RRID:SCR_012773

Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.

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C2C12 (tool)

RRID:CVCL_0188

Cell line C2C12 is a Spontaneously immortalized cell line with a species of origin Mus musculus (Mouse)

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