Hkera, a human transcriptome partitioner.

Developing a r eliable hous ekeeping ( HK) a nd t issue-specific ( TS) gene classifier is of importance because it can provide an initial clue to a gene’s cellular r ole an d f unction. W e d escribe h ere a n ovel H K/TS g ene cl assifier, called HKera, developed based on a n ovel property of HK genes that we have previously uncovered (Shaw et al., PLosONE e29314 (2011)), namely that the ranking or der of t heir e xpression l evels, a s opp osed t o t he e xpression l evels themselves, tends to be preserved from one tissue to another. Evaluated against multiple be nchmark s ets o f human H K genes, i ncluding one r ecently de rived from ne xt g eneration s equencing, H Kera w as s hown t o pe rform significantly better t han f ive ot her c lassifiers t hat us e di fferent methodologies. A n enrichment an alysis of pa thway a nd g ene o ntology a nnotations s howed t hat HKera-predicted HK and TS genes have distinct functional roles and, together, cover most of the ontology categories. These results show that HKera is a good human t ranscriptome pa rtitioner t hat c an be us ed t o s earch f or, a nd obtain useful expression and functional information for, novel HK (TS) genes.