Motifs

# These files are used for motif scanning of DNA using fimo in the MEME suite (see relevant documentation) # 1. Species-specific motif IDs, orthogrouping and cichlid gene IDs (Mz - M. zebra; Pn - p. nyererei; Ab - A. burtoni; Nb - N. brichardi; On - O. niloticus)merged_mat_qual_pvals_ALL.out1.TF.* # e.g. merged_mat_qual_pvals_ALL.out1.TF.ab # 2. MEME files of all motifs for motif scanning according to:# A) those derived from i) human-based and ii) mouse-based predictions based on orthology (see Methods); and# B) different confidence levels: 2a - cichlid-specific (CS) matrices; 2b - cichlid-wide (CW) matrices; and 2c - JASPAR matrices# Ai) Derived from HumanHumanDerived/2a_CS_*.memeHumanDerived/2b_CW_*.memeHumanDerived/2c_JASPAR_*.meme# all meta data on above motifs, including motifID, genesymbol, EnsemblID, orthoGroup, cichlid_geneIDs, collated Optimal p-values for scanningHumanDerived/cichlid_allHs_motifs_meta_info.txt# Aii) Derived from MouseMouseDerived/2a_CS_*.memeMouseDerived/2b_CW_*.memeMouseDerived/2c_JASPAR_*.meme# all meta data on above motifs, including motifID, genesymbol, EnsemblID, orthoGroup, cichlid_geneIDs, collated Optimal p-values for scanningMouseDerived/cichlid_allMm_motifs_meta_info.txt