Engineering:
- Document the code.
- Document the high-level "flow".
- Change DiseaseClass (or equivalent) to work for sources other than autworks.


Science:
- Get ranking for seeds in other sources.
- Did the schizophrenia verification set include known seeds?
- Does current algorithm optimize for sensitivity? If so, then consider optimizing for PPV instead.
- Is it a good idea to intersect the different sources used in the forming the interaction network?
- Or, explain why the current union of data sources for interaction network is a good idea
- Think about setting the thresholds using a statistical method, eg, hypergeometric or gene set enrichment analysis (GSEA)
- consider altering the structure of the interaction network as part of sensitivity analysis
- add figure: show small network with counts and paths


Writing:
- Describe how Assaf's PPI_File was created.
- Describe structure of the network (nodes, edges, number of connected
  components, average edges per node, distribution of number of edges
  per node, etc)
- Describe what is already known about using hub genes.


Future science:
- Use other measures than betweenness centrality.
- Consider using other sources for gene networks.
- Count repeated genes within a pair? Should we consider the
  relatedness between two genes?
- When searching through paths, should we retain only the shortest?
  Shortest + n? All? Other?
- Can we validate algorithm for disease where gene network is likely
  very complete?
- Is hold-out testing the best way to evaluate given that network for
  neuropsych genes is likely to be quite sparse?
- Should we remove disease specific genes from the entire graph before
  computing betweenness centrality (to increase signal)?


Known gene databases:
Assaf's
Reactome
http://string-db.org/
http://tools.autworks.hms.harvard.edu/genes/20692/gene_sets
https://gene.sfari.org/autdb/Welcome.do
http://www.szgene.org/
http://bioinfo.mc.vanderbilt.edu/SZGR/
phenopedia: (http://64.29.163.162:8080/HuGENavigator/phenoPedia.do?firstQuery=Schizophrenia&cuiID=C0036341%20%20&typeSubmit=GO&check=y&which=2&pubOrderType=pubD)

Interesting/Relevant websites:

http://www.nature.com/nrg/journal/v12/n1/full/nrg2918.html

http://www.ovarianresearch.com/content/pdf/1757-2215-6-92.pdf

http://www.biomedcentral.com/1471-2105/7/219

http://nar.oxfordjournals.org/content/early/2014/07/24/nar.gku678.full

http://www.biomedcentral.com/1752-0509/3/36/ <---- check this out

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ <----- Also this

http://www.biomedcentral.com/1752-0509/2/72

http://nar.oxfordjournals.org/content/37/suppl_2/W305.short

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0061505

http://bioinformatics.oxfordjournals.org/content/24/13/i277.long

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902235/

New gene?
http://www.news-medical.net/news/20140704/Researchers-reveal-how-schizophrenia-linked-genetic-variation-alters-skeletons-of-developing-brain-cells.aspx