Table 1.

Prostate cancer gene signatures evaluated

Signature No	Phenotype	Samples used to generate signature	Author	Available genes	In Network*
1	Aggressive disease	Divided 66 microdissected prostate cancer specimens into two groups based on clinical aggressiveness defined as prostate-specific antigen (PSA) relapse following radical retropubic prostatectomy (RRP), distant metastasis, or cancer invasion into adjacent organs	Yu et al28	26	Yes
2	Benign versus cancerous prostate tissue	Proteomic screen of microdissected prostate tissue embedded in tissue microarray for genes that best discriminated between benign, localized prostate cancer and metastatic disease	Bismar et al18	12	Yes
3	High-grade tumor	Examined 12 microdissected RRP Gleason pattern 3 specimens compared with that of 12 Gleason pattern 4 and eight Gleason pattern 5	True et al27	85	Yes
4	PTEN pathway/poor prognosis	Comparison of 35 phosphatase and tensin homolog (PTEN) negative and 70 PTEN positive based on immunohistochemistry from stage II estrogen receptor status-matched breast cancer specimens. Signature subsequently validated in a historic dataset of 79 prostate cancer specimens19 described above in the Sun et al signature	Saal et al24	184	Yes
5	Recurrence signature in solid tumors	Comparison of gene expression signature from 12 metastatic adenocarcinoma nodules from prostate and five other tissue types compared to 64 primary adenocarcinomas from primary tumors	Ramaswamy et al23	17	Yes
6	Recurrent/aggressive disease	Evaluated 62 primary prostate tumors, 41 normal prostate specimens and nine lymph node metastases to develop a two-gene model of recurrence	Lapointe et al21	2	No
7	Recurrent disease	79 patient RRP specimens from patients with clinically localized prostate cancer. 39 cases with recurrence defined as three consecutive elevations in PSA for at least 5 years	Sun and Goodison26	11	No
8	Recurrent disease	Using 21 prostate cancer samples, five genes using k-nn clustering were identified.	Singh et al25	5	No
9	Recurrent disease /High-Gleason score	512 candidate genes were analyzed for correlation with Gleason score from 71 patient RRP specimens (16 patients with relapsed disease defined as two consecutive PSA elevations over 84 months)	Bibikova et al16	16	Yes
10	Relapse-free survival	Using 21 prostate cancer samples from Singh et al, the authors identified three signatures of recurrence and subsequently validated these signatures on a set of 79 tumors	Glinsky et al19	4/4/5	No
11	Stem cell nature	Comparison of CD133+/α2β1hi cell culture specimens from 12 human prostate cancers compared with eight CD133–/α2β1low specimens.	Birnie et al17	22	Yes
12	Systemic disease after relapse, Sig 1	213 patients with prostate cancer PSA relapse and no evidence of systemic disease (defined as a positive bone scan or CT scan) were compared with 213 patients with prostate cancer with PSA relapse	Nakagawa et al22	17	No
13	Systemic disease after relapse, Sig 2	Reanalysis of the above Nagakawa et al (Mayo Clinic dataset) as described in the Methods section		133	Yes

^*In Network indicates that the listed gene signature connects to the Sanger cancer genes via SPAN and composes part of the interactor signature.