We perform our experiments on a database of note files we compiled from the Humdrum project library [19] described in Table 5.
As the TGF β regulated genes that we compiled from the microarray data above does not contain interaction information, we used Cytoscape with the MiMI plugin [28] to identify protein-protein interactions.
We compiled from the Paleobiology Database (http://paleodb.org) information on 3303 endemic and 2716 cosmopolitan marine genera from North America and 3788 endemic and 3360 cosmopolitan marine genera from Europe.
Because several studies had indicated a relationship between invasiveness in plants and seed mass [16], [17], [18] and chromosome number or ploidy [19], [20], [21], we compiled, from large online databases, values for both traits as predictor data.
In the first step, all RNA-tags were compared against a small subunit and a large subunit rRNA reference database (SSUrdb and LSUrdb, respectively) that we compiled from publicly available sources (SILVA[21], RDP-II[22], Genbank nucleotide; see materials and methods for details).
The phenotype information we compiled from these measurements was paired with the genotype information already generated by Alonso-Blanco et al. (1998) to create QTL maps.
These data are integrated with times series of SST, SSH, and OCC that we compile from satellite sensor data.
In our study, we compile from SNPedia and reference [ 64] a total of 53 reported susceptible SNPs, and 24 of them are found to be within 5 Mbp regions of 7 domains (i.e., HNF-1B_C, IF_tail, Sulfatase, Collagen, Alk_phosphatase, Pkinase_Tyr, and FGF) that are ranked among top 10.
In our study, we compile from SNPedia 36 reported susceptible SNPs, and 29 of them are found to be within 5 Mbp regions of 8 domains (i.e., Sulfatase, NACHT, Collagen, Crystall, Pkinase_Tyr, CARD, Gla, and Hormone_1) that are ranked among top 10.
In our study, we compile from SNPedia 60 reported susceptible SNPs, and 38 of them are found to be within 5 Mbp regions of 7 domains (i.e., Sulfatase, Pkinase_Tyr, Crystall, FGF, Collagen, NACHT, and Recep_L_domain) that are ranked among the top 10.
In our study, we compile from SNPedia 48 reported susceptible SNPs, and 25 of them are found to be within 5Mbp regions of 6 domains (i.e., NACHT, Recep_L_domain, Collagen, HNF-1A_C, CARD, and FGF) that are ranked among the top 10.
