Based on gene expression similarity clustering different subgroups can be identified, corresponding to the manually compiled ones in Figure 7.
As an alternative to the manually compiled set of complexes in CORUM, an independent set of putative complexes was computationally derived from high-throughput protein interaction experiments by identifying highly connected clusters of proteins in an extended network of human protein interactions [31].
The World Anti-Doping Agency (WADA) publishes the Prohibited List, a manually compiled international standard of substances and methods prohibited in-competition, out-of-competition and in particular sports.
We manually compiled the list of microRNAs that were reported in literature as differentially expressed (up- or down-regulated) in various cancers in human (Additional File 8).
Orthologous protein-coding genes in the two succinogens were manually compiled by comparing gene order, gene orientation (forward/reverse), features of intergenic regions, and protein similarity (minimum 25% identity at the protein level).
The ListeriaBase homepage features a brief description of the genus Listeria in the main panel along with manually compiled information that are related to Listeria such as news & conferences, blogs & other information and the most recent published papers in the side panel.
In the current version of BOSS, we manually compiled the list of objects from various biomedical information sources such as HGNC [ 10], GO (Gene Ontology) [ 11], MeSH [ 12], and FDA [ 13].
The gene sets whose enrichment was assessed were taken from the Molecular Signatures Database (Subramanian et al., 2005); in particular, we used a collection of canonical, manually compiled pathways (collection C2-CP).
The Version 2.5 of MSigDB contains 1,186 gene sets in the "C2: chemical and genetic perturbations" category [ 10], manually compiled from over 300 publications.
Additionally, the 2R-ohnologue complement of the human protein kinome was manually compiled by performing phylogenetic and gene synteny analyses of 2R-ohnologue families as in (1) (Supplementary Table S2).
