We here developed a web-based tool, PPI Finder, to mine human PPIs from PubMed abstracts based on their co-occurrences and interaction words, followed by evidences in human PPI databases and shared terms in GO database.
In this study, we addressed this question by using a DLPFC subregion-defined by 4 previous fMRI studies-as seed for connectivity-based parcellation and hence tested whether distinct subfoci could be identified based on their co-activation patterns across fMRI experiments in the BrainMap database.
This transcriptomics-based method allows the identification of genes involved in a defined metabolic pathway based on their co-expression with genes of known function, through the assumption that genes involved in the same biochemical pathway are co-regulated 34.
Determine the target gene group based on their co-expression in a common systemic response.
Engle and Granger [11] analyzed the linear combination of variables based on their co-integration relationship.
From our GS BC module construction, GSs (or BCs) are clustered together based on their co-expression pattern across all the ROIs in the whole brain (or across all the genes in the genome).
Two particular strengths of fMRI are that it is able to detect brain activation induced by a task, and provide the connectivity between populations of neurons based on their co-activation at resting state.
The method described above briefly consists of the following steps (details of which, related to the implementation we made, are given in the "Methods" section): 1. Determine the target gene group based on their co-expression in a common systemic response.
For this, we built a network of the hippocampus-selective genes based on their co-citation into the Pubmed database as well as the presence of specific transcription factor binding sites (TFBS) in their promoter regions ( Figure S1).
We tested several candidate peptides based on their co-occurence with CAPN3 or myopathy in PubMed abstracts, and found some of them to be cleaved by CAPN3 (Table 1) confirming the predictive potential of the motif.
A fraction of these cells are osteoprogenitors, based on their co-expression of sox9 and runx2 (Fig. 3C,E) and these cells appear to exploit the collagen rich matrix to sense their mechanical environment.
