From 3aee2fd43e3059a699af2b63c6f2395e5a55e515 Mon Sep 17 00:00:00 2001 From: KatolaZ Date: Wed, 27 Sep 2017 15:06:31 +0100 Subject: First commit on github -- NetBunch 1.0 --- doc/f3m.1.html | 235 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 235 insertions(+) create mode 100644 doc/f3m.1.html (limited to 'doc/f3m.1.html') diff --git a/doc/f3m.1.html b/doc/f3m.1.html new file mode 100644 index 0000000..3890394 --- /dev/null +++ b/doc/f3m.1.html @@ -0,0 +1,235 @@ + + + + + + f3m(1) - Count all the 3-node subgraphs of a directed graph + + + + + +
+ + + +
    +
  1. f3m(1)
    2. +
  2. www.complex-networks.net
    3. +
  3. f3m(1)
    4. +
+ +

NAME

+

+ f3m - Count all the 3-node subgraphs of a directed graph +

+ +

SYNOPSIS

+ +

f3m graph_in [num_random]

+ +

DESCRIPTION

+ +

f3m performs a motif analysis on graph_in, i.e., it counts all the +3-node subgraphs and computes the z-score of that count with respect +to the corresponding configuration model ensemble.

+ +

PARAMETERS

+ +
+
graph_in

input graph (edge list). It must be an existing file.

+
num_random

The number of random graphs to sample from the configuration model + for the computation of the z-score of the motifs.

+
+ + +

OUTPUT

+ +

f3m prints on the standard output a table with 13 rows, one for each +of the 13 possible 3-node motifs. Each line is in the format:

+ +
    motif_number  count  mean_rnd  std_rnd  z-score
+
+ +

where motif_number is a number between 1 and 13 that identifies the +motif (see MOTIF NUMBERS below), count is the number of +subgraphs ot type motif_number found in graph_in, mean_rnd is +the average number of subgraphs of type motif_number in the +corresponding configuration model ensemble, and std_rnd is the +associated standard deviation. Finally, z-score is the quantity:

+ +
   (count - mean_rnd) / std_rnd
+
+ +

The program also prints a progress bar on STDERR.

+ +

MOTIF NUMBERS

+ +

We report below the correspondence between the 13 possible 3-node +subgraphs and the corresponding motif_number. In the diagrams, +'O--->O' indicates a single edge form the left node to the right node, +while 'O==O' indicates a double (bi-directional) edge between the +two nodes:

+ +
   (1)  O<---O--->O
+
+   (2)  O--->O--->O
+
+   (3)  O<==>O--->O
+
+   (4)  O--->O<---O
+
+   (5)  O--->O--->O
+         \        ^
+          \_______|
+
+   (6)  O<==>O--->O
+         \        ^
+          \_______|
+
+   (7)  O<==>O<---O
+
+   (8)  O<==>O<==>O
+
+   (9)  O<---O<---O
+         \        ^
+          \_______|
+
+  (10)  O<==>O<---O
+         \        ^
+          \_______|
+
+  (11)  O--->O<==>O
+         \        ^
+          \_______|
+
+  (12)  O<==>O<==>O
+         \        ^
+          \_______|
+
+  (13)  O<==>O<==>O
+        ^\       ^/ 
+         \\_____//
+          \_____/
+
+ +

EXAMPLES

+ +

To perform a motif analysis on the E.coli transcription regulation +graph, using 1000 randomised networks, we run the command:

+ +
    $ f3m e_coli.net 1000
+    1          4760         4400.11    137.679     +2.614
+    2           162          188.78      8.022     -3.338
+    3             0            0.89      3.903     -0.228
+    4           226          238.32      7.657     -1.609
+    5            40            6.54      2.836    +11.800
+    6             0            0.01      0.077     -0.078
+    7             0            0.12      0.642     -0.192
+    8             0            0.00      0.032     -0.032
+    9             0            0.01      0.109     -0.110
+    10            0            0.00      0.000     +0.000
+    11            0            0.00      0.032     -0.032
+    12            0            0.00      0.000     +0.000
+    13            0            0.00      0.000     +0.000
+    $
+
+ +

Notice that the motif 5 (the so-called "feed-forward loop") has a +z-score equal to 11.8, meaning that it is highly overrepresented in +the E.coli graph with respect to the corresponding configuration model +ensemble. Conversely, the motif 2 (three-node chain) is +underrepresented, as made evident by value of the z-score (-3.338).

+ +

SEE ALSO

+ +

johnson_cycles(1)

+ +

REFERENCES

+ + + + +

AUTHORS

+ +

(c) Vincenzo 'KatolaZ' Nicosia 2009-2017 <v.nicosia@qmul.ac.uk>.

+ + +
    +
  1. www.complex-networks.net
    2. +
  2. September 2017
    3. +
  3. f3m(1)
    4. +
+ +
+ + -- cgit v1.2.3