About 31% of human gene names do not appear in MEDLINE, nor do approximately 90% of human non-coding RNAs. And existing literature is heavily skewed towards well-known genes with 75% of effort focusing on 10% of genes (Edwards et al., 2011).
(e.g., synaptic transmission, sarcopenia). We have developed software that analyzes over 75,000 human microarray experiments to identify genes correlated across heterogeneous conditions (Dozmorov & Wren, 2011a,b; Wren, 2009) that can then be linked back to what they have in common in MEDLINE (Figure). Phenotype prediction has been 85% accurate in wet-lab experiments (48 positive out of 56 tested) and several formerly uncharacterized genes successfully validated (Towner et al, 2013a; Towner et al., 2013b; Clemmensen et al., 2012; Lupu et al., 2011; Daum et al., 2009).
Clemmensen, S.N., Bohr, C.T., Rorvig, S., Glenthoj, A., Mora-Jensen, H., Cramer, E.P., Jacobsen, L.C., Larsen, M.T., Cowland, J.B., Tanassi, J.T. et al. (2012). Olfactomedin 4 defines a subset of human neutrophils.
J. Leukocyte Biol. 91, 495-500.
Daum, J.R., Wren, J.D., Daniel, J.J., Sivakumar, S., McAvoy, J.N., Potapova, T.A., and Gorbsky, G.J. (2009). Ska3 is required for spindle checkpoint silencing and the maintenance of chromosome cohesion in mitosis.
Current Biol. 19,1467-1472.
Dozmorov, M.G., and Wren, J.D. (2011a) High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses.
BMC Bioinformatics 12 Suppl 10:S2.
Dozmorov, M.G., Giles, C.B., and Wren, J.D. (2011b). Predicting gene ontology from a global meta-analysis of 1-color microarray experiments.
BMC Bioinformatics 12 Suppl 10:S14.
Edwards, A.M., Isserlin, R., Bader, G.D., Frye, S.V., Willson, T.M., and Yu, F.H. (2011). Too many roads not taken.
Lupu, C., Zhu, H., Popescu, N.I., Wren, J.D., and Lupu, F. (2011). Novel protein ADTRP regulates TFPI expression and function in human endothelial cells in normal conditions and in response to androgen.
Blood 118, 4463-4471.
Towner, R.A., Jensen, R.L., Vaillant, B., Colman, H., Saunders, D., Giles, C.B., and Wren, J.D. (2013a) Experimental validation of 5 in-silico predicted glioma biomarkers.
Towner, R.A., Jensen, R.L., Colman, H., Vaillant, B., Smith, N., Casteel, R., Saunders, D., Gillespie, D.L., Silasi-Mansat, R., Lupu, F. et al. (2013b). ELTD1, a potential new biomarker for gliomas.
Wren, J.D. (2009). A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide.