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 Human
HumanDerived/2a_CS_*.meme
HumanDerived/2b_CW_*.meme
HumanDerived/2c_JASPAR_*.meme
# all meta data on above motifs, including motifID, genesymbol, EnsemblID, orthoGroup, cichlid_geneIDs, collated Optimal p-values for scanning
HumanDerived/cichlid_allHs_motifs_meta_info.txt

# Aii) Derived from Mouse
MouseDerived/2a_CS_*.meme
MouseDerived/2b_CW_*.meme
MouseDerived/2c_JASPAR_*.meme
# all meta data on above motifs, including motifID, genesymbol, EnsemblID, orthoGroup, cichlid_geneIDs, collated Optimal p-values for scanning
MouseDerived/cichlid_allMm_motifs_meta_info.txt