Research Blog
Paper
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.
Overrepresentation
Jul 19th
Stats
Jul 13th
Motif A (Chlorpromazine):
- There are 86 Edges and 76 Nodes in total in the neighbourhood for this motif. (162)
- The similarity between the compound Chlorpromazine and Trimeprazine has a 0.85 Tanimoto co-efficient.
- There are 60 other compounds that bind to the H1 Histamine Receptor.
- Chlorpomazine has 3 other similar drugs. (Tanimoto is 0.85 for all)
- Trimeprazine is similar to 4 additional compounds. Tanimoto betweeen 0.87 – 1.0.
- The H1 Histamine Receptor has 1 additional target and is associated with 2 proteins one of which has a similar structure.
Motif A (Lenalidomide)
- Total of 21 Nodes and 25 Edges in this motif. (46)
- Lenalidomide has 1 additional target.
- Talidomide has 2 additional targets.
- 0.85 is the tanimoto coefficient in both directions if Lenalidomide and Talidomide.
- TNF has 14 other drugs that bind to it and 1 Protein.
Motif C (Isradipine)
- Blast score between CACH2 and SCN4A is 2.0E-63.
- Blast score in the reverse direction is 1.0E-59.
Motif Examples
Jul 12th
Looked at results for some good “known” off-label for each type of motif to write about in the paper.
- MotifA - Lenalidomide <–> Thalidomide –> TNF [Multiple Myeloma among other things]
- MotifB - Topiramate
- MotifC - Isradipine [Heart/Blood Pressure and Parkinson's Disease/ ~Paralysis]
Ideas for the scoring section of the paper:
- Check the values such as Tanimoto, BLAST and G-Sesame known motifs (i.e. Chlorpromazine)
- Is there any differentation between a known motif and a random unsignificant motif
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);
