Motifs

# These files are used for motif scanning of DNA using fimo in the MEME suite (see relevant documentation) <br><br># 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)<br><br>merged_mat_qual_pvals_ALL.out1.TF.* # e.g. merged_mat_qual_pvals_ALL.out1.TF.ab <br><br><br># 2. MEME files of all motifs for motif scanning according to:<br># A) those derived from i) human-based and ii) mouse-based predictions based on orthology (see Methods); and<br># B) different confidence levels: 2a - cichlid-specific (CS) matrices; 2b - cichlid-wide (CW) matrices; and 2c - JASPAR matrices<br><br><br># Ai) Derived from Human<br>HumanDerived/2a_CS_*.meme<br>HumanDerived/2b_CW_*.meme<br>HumanDerived/2c_JASPAR_*.meme<br># all meta data on above motifs, including motifID, genesymbol, EnsemblID, orthoGroup, cichlid_geneIDs, collated Optimal p-values for scanning<br>HumanDerived/cichlid_allHs_motifs_meta_info.txt<br><br># Aii) Derived from Mouse<br>MouseDerived/2a_CS_*.meme<br>MouseDerived/2b_CW_*.meme<br>MouseDerived/2c_JASPAR_*.meme<br># all meta data on above motifs, including motifID, genesymbol, EnsemblID, orthoGroup, cichlid_geneIDs, collated Optimal p-values for scanning<br>MouseDerived/cichlid_allMm_motifs_meta_info.txt