There are 13 files associated with each genome:

[1] XXX.orthomap
================

Sample line:
16128415	16123328

Pattern:
GI-Ecoli \t GI-XXX

Description:
This file contains the orthology mapping information.
The numbers are GenBank identifiers (GI numbers)

[2] XXX.status
==============

Sample: 
16120787	16122488	16132218	16129569	0F:0S:0M	0F:1S:0M	

Pattern:
TF-XXX \t TG-XXX \t TF-Ecoli \t TG-Ecoli \t Motif status-XXX \t Motif status Ecoli

Description:
TF=transcription factor; TG=target gene
Each interaction from Tf -> Tg is shown here.

Motif status-XXX: Types of motifs this interaction participates
in the reconstructed network of the genome of interest.
0F:0S:0M - means this interaction does not participate in any
motif in the reconstructed network

Motif status-Ecoli: Types of motifs this interaction participates
in the Ecoli network.
0F:1S:0M - means that this interaction forms a part of 1 single input
motif

[3] XXX.tf.gi.txt
=================

Sample:
gi|21672894|ref|NP_660959.1|

Pattern:
GI1

Description:
GI number of the predicted transcription factors in the genome of interest.

[4] XXX.rnet.txt
================

Sample:
16120787        16122488        16132218        16129569

Pattern:
TF-XXX \t TG-XXX \t TF-Ecoli \t TG-Ecoli

Description:
TF=transcription factor; TG=target gene
Each interaction from Tf -> Tg is shown here.

[5] XXX.rnet.noauto.txt
=======================

Same as [4] but does not contain autoregulation

[6] XXX.rnet.ff.txt
===================

Sample:
16120516	16120465	16123961

Pattern:
GI1 \t GI2 \t GI3

Description:
Feed forward motif representation
GI1 -> GI2 (GI1 regulates GI2)
GI1 -> GI3 (GI1 regulates GI3)
GI2 -> GI3 (GI2 regulates GI3)

[7] XXX.rnet.sim.txt
====================

Sample:
16123569	16123568 16123567

Pattern:
GI1 \t GI2 GI3 GI4 GIn

Description:
Single input motif
GI1 -> GI2, GI3, GI4, GIn
(GI1 regulates GI2, GI3, GI4, GIn)

[8] XXX.rnet.mim.txt
====================

Sample:
16120787:16120516	16123662:16124119

Pattern:
GI1:GI2 \t GI3:GI4

Description:
Multiple input motif
GI1 -> GI3, GI4 (GI1 regulates GI3, GI4)
GI2 -> GI3, GI4 (GI2 regulates GI3, GI4)

[9] XXX.tf.rnet.txt
===================

Same as XXX.rnet.txt
but this is restricted to the transcription
factor inter-regulatory network, i.e. where the
target gene is also a transcription factor.

[10] XXX.tf.rnet.noauto.txt
===========================

Same as XXX.rnet.noauto.txt
but this is restricted to the transcription
factor inter-regulatory network.

[11] XXX.tf.rnet.ff.txt
=======================

Same as XXX.rnet.ff.txt
but this is restricted to the transcription
factor inter-regulatory network.

[12] XXX.tf.rnet.sim.txt
=======================

Same as XXX.rnet.sim.txt
but this is restricted to the transcription
factor inter-regulatory network.

[13] XXX.tf.rnet.mim.txt
=======================

Same as XXX.rnet.mim.txt
but this is restricted to the transcription
factor inter-regulatory network.

If something is not clear, please contact:
M. Madan Babu
madanm AT mrc-lmb DOT cam DOT ac DOT uk