TABLE S4: Proliferation-related and chromosomal instability-related genes up-regulated in ATC (weight <4.0) 44-gene Unigene Prolif. Prolif. Gene Gene description and (GO biological process) Number N1 N2 N3 N4 ATC1 ATC2 ATC3 ATC4 ATC5 Cluster1 CIN702 Signature3 Normal tissues ATC samples ASF1B anti-silencing function 1 homolog B (unknown) Hs.26516 0.2 0.3 0.3 0.3 0.8 0.8 1.1 0.8 0.4 yes AURKB aurora kinase B (cell cycle) Hs.442658 0.06 0.06 0.08 0.05 2.4 1.2 0.003 0.6 0.6 yes yes yes BIRC5 baculoviral IAP repeat-containing 5 (anti apoptosis) Hs.514527 0.7 0.3 0.4 0.3 0.8 0.5 0.5 0.6 0.6 yes yes budding uninhibited by benzimidazoles 1 homolog (mitotic BUB1 spindle checkpoint) Hs.469649 0.06 0.04 0.02 0.05 1.8 1.0 0.6 0.5 0.5 yes yes CCNE1 cyclin E1 (cell cycle) Hs.244723 0.5 0.4 0.5 0.6 1.3 1.4 2.2 1.5 1.1 yes CCNF cyclin F (cell cycle) Hs.1973 0.1 0.1 0.2 0.3 0.7 1.0 1.0 0.8 1.2 yes yes CDC45L CDC45 cell division cycle 45-like (cell cycle) Hs.474217 0.1 0.1 0.1 0.3 1.6 0.7 0.5 0.9 0.8 yes CDC6 cell division cycle 6 homolog (cell cycle) Hs. 405958 0.08 0.08 0.08 0.07 0.3 0.8 0.5 0.6 1 yes yes CDC7 cell division cycle 7 (cell cycle) Hs.533573 0.2 0.2 0.2 0.1 0.5 0.9 1 0.6 1.3 yes CDKN3 cyclin-dependent kinase inhibitor 3 (cell cycle) Hs.84113 0.1 0.1 0.7 0.1 0.9 0.8 0.6 0.4 6.2 yes CHEK1 CHK1 checkpoint homolog (cell cycle) Hs. 24529 0.5 0.5 0.3 0.5 1.1 0.7 1.1 1.5 0.9 yes DKC1 dyskeratosis congenita 1 (cell proliferation) Hs. 4747 0.7 0.6 0.5 0.6 1.1 1.0 0.8 0.6 0.7 yes yes ESPL1 extra spindle poles like 1 (chromosome segregation) Hs.153479 0.2 0.3 0.3 0.4 0.4 0.6 1.2 0.7 0.9 yes yes FBXO5 F-box only protein 5 (cell cycle) Hs.645478 0.4 0.5 0.4 0.5 1.7 1.1 0.8 0.5 0.8 yes GPI glucose phosphate isomerase (carbohydrate metabolism) Hs. 466471 0.5 0.6 0.6 0.6 1.3 1.1 2 1.0 0.6 yes H2AFX H2A histone family, member X (DNA recombination) Hs. 477879 0.13 0.12 0.12 0.14 0.8 0.4 0.8 0.4 0.3 yes HDGF hepatoma-derived growth factor (cell proliferation) Hs.506748 0.5 0.5 0.4 0.6 1.0 0.7 0.9 1 0.5 yes KIAA0286 KIAA0286 protein (unknown) Hs.591040 0.5 0.5 0.4 0.4 0.6 0.6 1.0 0.4 0.6 yes KIF11 kinesin-like 1 (mitosis) Hs.8878 0.2 0.1 0.2 0.1 0.5 0.6 0.3 0.6 1.0 yes KIF23 Kinesin family member 23 (mitosis) Hs.270845 0. 04 0.02 0.04 0.05 0.6 0.7 0.4 0.9 0.5 yes KNTC2 Kinetochore associated 2 (cell cycle) Hs. 414407 0.1 0.6 0.3 0.1 0.8 1.5 1.7 0.7 1.1 yes MAD2L1 mitotic arrest deficient-like 1 (cell cycle) Hs.591697 0.06 0.06 0.07 0.09 0.6 0.4 0.3 0.4 0.5 yes yes yes MCM2 minichromosome maintenance deficient 2 (DNA replication) Hs.477481 0.002 0.0058 0.10 0.12 1.3 0.6 0.4 0.4 0.7 yes yes MCM3 minichromosome maintenance deficient 3 (DNA replication) Hs. 179565 0.7 0.6 0.5 0.5 0.9 1.7 1.9 0.9 1.1 yes yes MCM4 minichromosome maintenance deficient 4 (DNA replication) Hs. 460184 1.0 0.8 0.9 1.0 1.9 1.7 3.4 2 1.4 yes MKI67 antigen identified by monoclonal antibody Ki-67 (cell cycle) Hs.80976 0.3 0.1 0.4 0.1 0.6 0.6 0.8 1.0 0.9 yes MTCH2 mitochondrial carrier homolog 2 (transport) Hs. 269944 0.6 1.4 0.7 0.5 0.9 0.9 1.7 0.8 2.3 yes NCAPD2 non-SMC condensin I complex, subunit D2 (cell cycle) Hs. 5719 0.8 0.7 0.5 0.7 1.2 2.2 1.4 1.2 0.6 yes NUP205 nucleoporin 205kDa (transport) Hs.632299 0.6 0.5 0.4 0.5 1.0 0.7 1.0 0.7 0.7 yes ORC1L origin recognition complex, subunit 1-like (DNA replication) Hs.17908 0.9 0.7 0.7 0.7 0.9 1.2 2.2 1.4 1.2 yes PCNA proliferating cell nuclear antigen (DNA replication) Hs.147433 0.4 0.4 0.3 0.3 0.7 1.0 0.7 1.0 0.8 yes yes protein kinase, membrane associated tyrosine/threonine 1 (cell PKMYT1 cycle) Hs.77783 0.1 0.1 0.1 0.2 0.9 0.7 0.8 0.7 0.8 yes POLA polymerase (DNA directed), alpha (DNA replication) Hs.567319 0.6 1.2 0.9 0.8 0.7 2.5 2.4 1.3 1.4 yes RAE1 RAE1 RNA export 1 homolog (S. pombe) (RNA export) Hs.371698 0.5 0.5 0.5 0.5 0.5 0.8 0.8 1.0 0.8 yes RANBP1 RAN binding protein 1 (transport) Hs.24763 0.2 0.2 0.2 0.2 0.3 0.4 0.6 0.5 0.4 yes RRM1 ribonucleotide reductase M1 polypeptide (DNA replication) Hs.558393 0.3 0.2 0.2 0.2 2.7 1.0 0.6 0.7 0.5 yes yes yes RRM2 ribonucleotide reductase M2 polypeptide (DNA replication) Hs.226390 0.8 0.8 0.7 1.0 1.4 1.9 6.5 1.6 1.5 yes yes yes SMC1 structural maintenance of chromosomes 1-like 1 (yeast) SMC1L1 (cell cycle) Hs.211602 0.8 0.8 0.6 0.8 0.9 1.9 1.6 1.2 1.6 yes TIMELESS timeless homolog (Drosophila) (development) Hs.118631 1.0 1.0 0.9 1.3 2.6 4.4 6.6 1.6 2.7 yes TIMP1 TIMP metallopeptidase inhibitor 1 (cell proliferation) Hs. 522632 1.1 1.7 1.7 1.5 32.3 6 19 10.9 6 yes TRIP13 thyroid hormone receptor interactor 13 (gene transcription) Hs.436187 0.3 0.2 0.2 0.3 0.8 0.8 0.5 0.8 0.8 yes yes yes UNG uracil-DNA glycosylase (base excision repair) Hs. 191334 0.1 0.1 0.4 0.4 0.4 0.4 1.7 0.3 1.0 yes yes VRK1 vaccinia related kinase 1 Hs.422662 0.6 0.6 0.6 0.5 1.0 1.4 1.5 1.0 1.4 yes 1. 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