1b.Network_Reconstruction_files

In Network_Reconstruction_files.tgz are the major files required to run network reconstruction and some output files:<br>- geneNamesTree # gene orthology of cichlid IDs, Ensembl IDs and gene descriptions<br>- Hs-Mm_EnsemblOrthology.txt # Ensembl orthology of Human and Mouse gene IDs<br>- full_orthologs_map3c.txt # contains the published orthologs gene IDs for mapping used previously<br>- list_k10 # list of k10 module numbers<br>- list_species # list of species<br>- OGIDS.txt # orthogroups<br>- OGIDS.txt5 # processed orthogroups file<br>- *_07.extrap.annotations.blast_out # extrapolation of motifs in cichlid gene promoters using human and mouse orthology <br>- mz-speciesspecnames_clusterassign.txt # Arboretum module assignment of M. zebra genes<br>- pn-speciesspecnames_clusterassign.txt # Arboretum module assignment of P. nyererei genes<br>- ab-speciesspecnames_clusterassign.txt # Arboretum module assignment of A. burtoni genes<br>- nb-speciesspecnames_clusterassign.txt # Arboretum module assignment of N. brichardi genes<br>- on-speciesspecnames_clusterassign.txt # Arboretum module assignment of O. niloticus genes<br>- geneNamesMapping.txt # gene orthology of cichlid IDs, Ensembl IDs and gene descriptions<br>- 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<br>- motifenr_merged-TFBSs_map2d.txt # output of processing files in TFBSs - Motif Discovery in gene promoter regions<br>- tftgco_merged.txt # output of processing TF-TG co-expression files