Human KRAB-A, KRAB-B, KRAB-b, KRAB-C, KRAB-L, BTB/POZ, SCAN, and FINGER HMM matrices were retrieved from previous analysis (Huntley et al. 2006).
Position-specific count matrices were retrieved from TRANSFAC database v12.1 [ 19] for the octamer (TRANSFAC id V$OCT_Q6) and the SOX-OCT joined motifs (TRANSFAC ids V$OCT4_02 and V$OCT4_01).
Once the empirical covariance matrix S is calculated from the expression data and the prior information matrix P retrieved from the prior network, we estimate the true network using glasso and wglasso.
end{aligned} (4 The rotation matrix can be retrieved from the quaternion as (R = (q_0^2-e^Te)I_3 + 2ee^T + 2q_0left[ etimes right]) [22].
As the information in the adjacency matrix has been retrieved from STRING, clusters reflect that neighboring genes on the list cooperate in biological functions.
As mentioned in the Materials and Methods, we used 64×4 substitution matrices estimated from substitutions retrieved from genic- and nongenic-DNA alignments previously grouped by GC content, to generate non-genic and coding sequences in which every site was hit at least ten times.
To further elucidate which proteins build up the notochordal sheath, extracellular matrix (ECM) genes were retrieved from the annotated RNA-seq pool using Gene Ontology.
TF identification: TRANSFAC Professional 11.4 was used as described previously [ 22] except that it was done with the set of all fungal TF binding sites retrieved from matrix.dat in TRANSFAC.
Alignment was made with ClustalW v.2.1 software (http://www.clustal.org) implemented on Linux command line interface, and a similarity matrix was generated with sequences retrieved from the GenBank database.
diazotrophicus PAl 5, G. oxydans H24, Ac. pasteurianus IFO 3283-01, and Granulibacter bethesdensis strain genomes; the relative presence/absence informations were retrieved from the OrthoMCL matrix generated above and organized in a new matrix.
