Research Blog
Bioinformatics
Changes
Aug 3rd
A new table of drugs for type C:
200 Motifs Identified:
Seen Compound Name
24 Mibefradil(118694)
24 Nicardipine(121098)
24 Isradipine(118056)
24 Ibutilide(118077)
24 Magnesium Sulfate(118260)
20 Tirofiban(118330)
20 Eptifibatide(117946)
7 Arsenic trioxide(118576)
6 Thiamine(117201)
4 Ridogrel(118597)
4 K-252a(119055)
4 Dazoxiben(119492)
3 Probenecid(118489)
2 2H-1-BENZOPYRAN-2-ONE(120274)
2 Biotin(120771)
2 Methoxsalen(118205)
1 Hyperforin(118928)
1 SR12813(120172)
1 Ethinyl Estradiol(116726)
1 Estradiol(116747)
1 Rifampin(117495)
1 Vitamin E(117996)
FANMOD with 1000 random
Aug 2nd
Result Overview:
Network name: D:\drugdatasetinput.txt
Network type: Directed
Number of nodes: 121320
Number of edges: 434800
Number of single edges: 307859
Number of mutual edges: 126941
Algorithm: enumeration
Subgraph size: 3
Generated 1000 random networks
with locally constant number of bidirectional edges,
3 exchanges per edge and 3 tries per edge.
172022813 subgraphs were enumerated in the original network.
197199994016 subgraphs were enumerated in the random networks.
197372016829 subgraphs were enumerated in all networks.
For the random networks: 1578398185 tries were made, 1274251639 were successful.
Randomization took 30053.2 seconds.
Enumeration took 697127 seconds.
Output Files:
Papers
Jul 5th
Some papers
- Itzkovic, S. and Alon, U. (2005) Subgraphs and network motifs in geometric networks. Physical Review. 71(2)
- Wernicke, S. (2006) Efficient Detection of Network Motifs. Transactions On Computational Biology and Bioinformatics. 3(4):347-359
http://www.slideshare.net/florianmarkowetz/network-biology-lent-2010-lecture-1-3322887
DOT Export appears to work but the file output needs the semantics removed (e.g. node24 [label="Compound 24", shape=box, color=white, width=1.63, height=1.63, fixedsize="true"]).
Stats
Jul 1st
- 4842 – Drugs
- 3500 – Targets
- 10743 – bi_to
- 274607 – h_s_s
With this information how likely/often will a motif appear in the dataset.
ONDEXView hss = graph.getRelationsOfRelationType(graph.getMetaData().getRelationType("h_s_s"));
int j = 0;
for (ONDEXRelation r : hss) {
ONDEXConcept to = r.getToConcept();
ONDEXConcept from = r.getFromConcept();
if (to.getOfType().getId().equals("Protein") && from.getOfType().getId().equals("Protein")) {
j++;
}
}
System.out.println("hss " + j);
Network Motif Finder
Jun 29th
Main problem is fileformats.
- MAVisto – .GML, .NET, .TXT
- Kavosh – ?
- FANMOD – txt
- Pajak – .net, .mat, .vgr, .ged, .dat, .mac, .mol
- mFinder – (Died)
- Cytoscape ->ClusterViz, Nemo, etc… (http://cytoscape.org/plugins2.php)
Tried converting to .dot directly in Ondex. However it doesn’t appear to have worked correctly (only nodes worked in Cytoscape)
Network motif analysis of a multi-mode genetic-interaction network
Network Motifs: Simple Building Blocks of Complex Networks
Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs
Wernicke S A faster algorithm for detecting network motifs. In Proceedings of the 5th Workshop on Algorithms in Bioinformatics: October 3-6, 2005; Mallorca, Spain. Berlin: Springer-Verlag; 2005:165-177.
