For example, it has become routine experimental practice to comprehensively analyze DNA, RNA, protein, regulation, and mutant phenotypes, facilitating a level of biological inference at the "system level".
Unlike previous methods that often use custom approaches that are organism specific, our method uses generalized linear models and extensions of standard reversible jump Markov chain Monte Carlo methods that can be readily extended to other organisms for a variety of biological inference problems relating to cell fate specification.
The novel association of the oncogenic pathway activation status with a phenotype "captured" by a marker 19-gene profile, of which none of the pathway genes is a member, demonstrates that biological inference in microarray studies should not be limited to the frequently applied approach of screening a list of top marker genes in a prognostic signature.
Beyond having data in hand, biological inference requires a wide range of skills and expertise.
For our method, we added P2 as a complementary algorithm to improve the biological inference.
Functional annotation and biological inference based on a single gene expression dataset has limitations due to experimental noise [ 4].
Moreover, the presence of coexpression links in multiple datasets alleviates the problems associated with biological inference based on a single gene expression data.
In the above-mentioned studies [ 1- 7], surgical procedures have been grouped and analysed according to gross anatomical regions (e.g., thyroid, gallbladder, prostate, etc)., which limits an interpretation of results based on biological inference.
These were identified a priori from previous studies and from biological inference (Rothman, 1986).
Even after the metabolomics community has databases to corral its data, Patrick notes that "an overarching challenge for systems biology is biological inference"—giving context and meaning to large amounts of data.
In contrast, biological inference is concerned with an understanding of how patterns in genomics data actually translate into the details of gene transcription, protein creation, and metabolism.
