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Enriched biological processes and molecular functions using Gene Ontology database.
To organize the data in Supplementary Table S1, proteins were classified into their respective molecular functions using PANTHER [25].
All the 67 up-regulated and 73 down-regulated genes were separately grouped into molecular functions using the GO Tool Box.
Genes were categorized based on their molecular functions using the software, mapped onto genetic networks in the IPA database and then ranked by score.
We then analyzed the induced and repressed genes for specific enrichment of defined biological processes and molecular functions using the Panther database [28].
Differentially expressed proteins were classified according to their main biological processes as well as their molecular functions using Swiss-Prot (http://www.uniprot.org/).org/
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Differentially expressed genes were classified according to the Gene Ontology functional category based on molecular function using DAVID (The Database for Annotation, Visualization and Integrated Discovery) [ 59].
The subfamilies are a subset of selected proteins that can be associated with functional classification (cellular process and molecular function) using manual expert curation.
Probe sets assigned with a gene symbol were functionally classified according to biological process and molecular function using Netaffx Analysis Center [ 34].
The differentially expressed proteins obtained from these searches were analyzed further for functional categorization based on biological processes and molecular function using annotations in HPRD [ 32].
Figure 2A summarises the annotation of the E-dependent DEG list with a Molecular Function using GO.
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