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Open Access Highly Accessed Methodology article

Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties

Yuanhua Liu1*, Valentina Devescovi1, Suning Chen2 and Christine Nardini1*

Author Affiliations

1 Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China

2 First Affiliated Hospital of Suzhou University, Jiangsu Institute of Hematology, , Suzhou, China

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BMC Systems Biology 2013, 7:14  doi:10.1186/1752-0509-7-14

Published: 19 February 2013

Additional files

Additional file 1:

Key molecules of melanoma identified using the FA based joint and separate analysis for NCI datasets. This.xls file has two sheets.The first one, named Joint, listed the molecules identified using the FA based integrated method (joint analysis). All the molecules are identified as a whole, but divided into three groups with the headers mRNA, miRNA and protein, respectively, in this sheet. The second sheet, named Separate, includes the molecules identified using the separate method. Each column represents one set of molecules resulted from one single omic dataset.

Format: XLS Size: 42KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Key molecules and functional annotations for the factors in M 13 resulted from TCGA datasets. This.xls file has four sheets. The first one, named mRNA lists, listed the mRNAs identified for the factors (from F 1 to F 13) in M 13 using the FA based integrated method (joint analysis), each column includes the key mRNAs for one factor. The second sheet, named miRNA lists is to list the miRNAs for each factor. The third sheet, named FuncAnnos of mRNAs, are the functional analysis results of mRNAs, where the mRNAs of each factor are annotated using DAVID annotation tool to identify the significantly enriched terms. The last sheet, named FuncAnnos of mRNAs&miRNAs, are the functional annotations of the integration of mRNAs and miRNAs for F 7 and F 8, where mRNAs and miRNA targets predicted using TargetScan are merged for DAVID functional analysis.

Format: XLS Size: 195KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data