Semantic Motif Hunting
Research Blog
Website Overview
Oct 6th
A quick website overviewing this project was developed and I never posted about it here, view it here.
For more information about this project contact Newcastle University’s Bioinformatics Support Unit.
Semantic integrity
Aug 13th
Type A
- 24,499
- 30,231 (10%+) – When drug1 binds to target.
Type B
- 19,185
- 22,864 (16%+) – When drug may bind to target2
Type C
- 70,715
- 70,866 (0.2%) – Protein cross checks to Diseases removed
- 200 (-99.7%) – h_s_s between target and protein2 removed
- 1,458,707 (1,963%+) – data includes targets that are “is_a” and/or show simiarity.
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:
FANMOD et al.
Jul 20th
FANMOD
Size 3 Subgraph (100,000 Samples, 100 Random Network)
- Approximate number of subgraphs: 265326840 (based on 100000 samples)
- 172022813 subgraphs were enumerated in the original network.
- Result File
Size 6 Subgraph (100,000 Samples, 100 Random Network)
- Approximate number of subgraphs: 9365924517517080 (based on 100000 samples)
MFINDER1.2
3 (Default Settings)
- -
6 (Default Settings)
- -
Overrepresentation
Jul 19th
