Description
The MotifLabMotif format is the default format for motifs used by
MotifLab, and it is currently the only format that will include information
about all the properties related to a motif (and not just the identifier
and matrix).
The format is basically a direct extension of the
INCLUSive
Motif Model format but with additional #-fields describing both
standard and user-defined motif properties such as the name of the
transcription factor (
#Short and
#Long), the transcription factor class
(
#Class), binding factors (
#Factors), the organisms the TFs are expressed
in (
#Organisms), motifs for known interacting factors (
#Interactions) and
alternative motifs models for the same TFs
(
#Alternatives). A file in MotifLabMotif format must start with a header line
reading "
#MotifLabMotif" which serves to identify the format.
Example:
#MotifLabMotif (inspired by INCLUSive Motif Model v1.0)
#
#ID = M00002
#Short = V$E47_01
#Long = E47 (E2A immunoglobulin enhancer binding factor)
#W = 15
#Class = 1.2.1.0
#Factors = E47
#Organisms = human (Homo sapiens)
#Interactions = M00001,M00002,M00058,M00065,M00066,M00068,MA0048,MA0081,M00454,MA0092
#Alternatives = M00065,M00066,M00071,M00222,MA0091
#Transfac class = C0010
4.0 4.0 3.0 0.0
2.0 5.0 4.0 0.0
3.0 2.0 4.0 2.0
2.0 0.0 9.0 0.0
0.0 11.0 0.0 0.0
11.0 0.0 0.0 0.0
0.0 0.0 11.0 0.0
1.0 2.0 8.0 0.0
0.0 0.0 0.0 11.0
0.0 0.0 11.0 0.0
0.0 0.0 4.0 7.0
1.0 4.0 3.0 3.0
1.0 6.0 2.0 2.0
1.0 4.0 4.0 2.0
1.0 4.0 2.0 3.0
#ID = M00001
#Short = V$MYOD_01
#Long = MyoD (myoblast determination gene product)
#W = 12
#Class = 1.2.2.0
#Factors = MyoD,MyoD (376 AA),MyoD (275 AA)
#Organisms = chick (Gallus gallus),rat (Rattus norvegicus),human (Homo sapiens)
#Interactions = M00001,M00002,M00004,M00006,M00222,M00223,M00225,M00231,M00232
#Alternatives = M00184
#Transfac class = C0010
1.0 2.0 2.0 0.0
2.0 1.0 2.0 0.0
3.0 0.0 1.0 1.0
0.0 5.0 0.0 0.0
5.0 0.0 0.0 0.0
0.0 0.0 4.0 1.0
0.0 1.0 4.0 0.0
0.0 0.0 0.0 5.0
0.0 0.0 5.0 0.0
0.0 1.0 2.0 2.0
0.0 2.0 0.0 3.0
1.0 0.0 3.0 1.0