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We then considered how these proteins, occurring in both environments, are distributed across the GO slim function and process terms obtained from TAIR (Berardini et al., 2004).
For example, retrieval of all human (taxonomy ID: 9606) genes having GO slim function including the word "transport" is as simple as http://link.g-language.org/9606/filter=GOslim_function:transport/format=tsv/.
Interestingly the Orthogroups shared in the interaction of T. versicolor with both hosts are overrepresented by "transcription factor activity" GO Slim Function terms (Additional file 4: Figure S3A: column B and 3D: column F) and underrepresented by "transport" GO Slim Process terms (Additional file 4: Figure 3: column B and 3F: column F).
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Finally, the GO-slim function was used to summarize the annotation results.
After refinement of the annotation results by GO-Slim function, the plot of transcripts GO classifications was constructed using Web Gene Ontology Annotation Plot WEGOO) software (Ye et al. 2006).
When GO Slim (Molecular Function) was used to compare gene ontology in control animals compared with those treated at -7°C and also those of the 0.2 salt group, there was virtually no difference in the relative partitioning between different functions under the two different treatments.
The SLiM discovery functions of SLiMScape have also been extended through the incorporation of QSLiMFinder and enrichment statistics for known SLiMs using SLiMProb (formerly called SLiMSearch 1.x).
It's true that the alpha keys are all of a good size, although others are noticeably slim, and the function keys have been dropped altogether: the Fn modifier activates hardware-related shortcuts mapped onto the keyboard, with no facility to call up the usual F1-F12 keys.
Gene ontology (GO) terms, GO Slim terms, and functions associated with each gene were subsequently identified.
Inhibitory activity of SLiMs on Hox protein function can be reconsidered in the light of previous functional data.
The GO terms were reclassified into different functional groups based on a set of GO slims in the Molecular Function and Biological Process categories in order to provide a broad overview of the ontology content of the final platform.
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