1b.Network_Reconstruction_files

In Network_Reconstruction_files.tgz are the major files required to run network reconstruction and some output files:- geneNamesTree # gene orthology of cichlid IDs, Ensembl IDs and gene descriptions- Hs-Mm_EnsemblOrthology.txt # Ensembl orthology of Human and Mouse gene IDs- full_orthologs_map3c.txt # contains the published orthologs gene IDs for mapping used previously- list_k10 # list of k10 module numbers- list_species # list of species- OGIDS.txt # orthogroups- OGIDS.txt5 # processed orthogroups file- *_07.extrap.annotations.blast_out # extrapolation of motifs in cichlid gene promoters using human and mouse orthology - mz-speciesspecnames_clusterassign.txt # Arboretum module assignment of M. zebra genes- pn-speciesspecnames_clusterassign.txt # Arboretum module assignment of P. nyererei genes- ab-speciesspecnames_clusterassign.txt # Arboretum module assignment of A. burtoni genes- nb-speciesspecnames_clusterassign.txt # Arboretum module assignment of N. brichardi genes- on-speciesspecnames_clusterassign.txt # Arboretum module assignment of O. niloticus genes- geneNamesMapping.txt # gene orthology of cichlid IDs, Ensembl IDs and gene descriptions- MzPnAbNbOnGenome-BLAST_PresentNULLOGIDS-noCand-noTF.txt2 # 4209 orthogroups with NULL orthogroup IDs for one or species are actually present in the genome (mis-annotations etc.) and not lost/absent- motifenr_merged-TFBSs_map2d.txt # output of processing files in TFBSs - Motif Discovery in gene promoter regions- tftgco_merged.txt # output of processing TF-TG co-expression files