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(12) Patent Application Publication (10) Pub. No.: US 2006/0068405 A1 Diber Et Al

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(12) Patent Application Publication (10) Pub. No.: US 2006/0068405 A1 Diber Et Al US 2006.0068405A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2006/0068405 A1 Diber et al. (43) Pub. Date: Mar. 30, 2006 (54) METHODS AND SYSTEMIS FOR Correspondence Address: ANNOTATING BOMOLECULAR Martin D. Moynihan SEQUENCES PRTSI, Inc. (76) Inventors: Alex Diber, Rishon-LeZion (IL); Sarah P.O. Box 16446 Pollock, Tel-Aviv (IL); Zurit Levine, Arlington, VA 22215 (US) Herzlia (IL); Sergey Nemzer, RaAnana (IL); Vladimir Grebinskiy, Highland Park, NJ (US); Brian Meloon, (21) Appl. No.: 11/043,860 Plainsboro, NJ (US); Andrew Olson, Northport, NY (US): Avi Rosenberg, Kfar Saba (IL); Ami Haviv, (22) Filed: Jan. 27, 2005 Hod-HaSharon (IL); Shaul Zevin, Mevaseret Zion (IL); Tomer Zekharia, Givataim (IL); Zipi Shaked, Tel-Aviv (IL); Moshe Olshansky, Haifa (IL); Related U.S. Application Data Ariel Farkash, Haifa (IL); Eyal Privman, Tel-Aviv (IL); Amit Novik, (60) Provisional application No. 60/539,129, filed on Jan. Beit-YeHoshua (IL); Naomi Keren, 27, 2004. Givat Shmuel (IL); Gad S. Cojocaru, Ramat-HaSharon (IL); Pinch as Akiva, Publication Classification Ramat-Gan (IL); Yossi Cohen, Surrey (GB); Ronen Shemesh, Modi In (IL); (51) Int. C. Osnat Sella-Tavor, Kfar-Kish (IL); CI2O I/68 (2006.01) Liat Mintz, East brunswick, NJ (US); G06F 9/00 (2006.01) Hanging Xie, Lambertville, NJ (US); Dvir Dahary, Tel-Aviv (IL); Erez (52) U.S. Cl. ................................................... 435/6; 702/20 Levanon, Petach-Tikva (IL); Shiri Freilich, Haifa (IL); Nili Beck, Kfar Saba (IL); Wei-Yong Zhu, Plainsboro, (57) ABSTRACT NJ (US); Alon Wasserman, New York, NY (US); Chen Chermesh, Mishmar HaShiva (IL); Idit Azar, Tel-Aviv (IL); Polypeptide sequences and polynucleotide sequences are Rotem Sorek, Rechovot (IL); Jeanne provided. Also provided are annotative information concern Bernstein, Kfar Yona (IL) ing Such sequences and uses for these sequences. Patent Application Publication Mar. 30, 2006 Sheet 1 of 50 US 2006/0068405 A1 S1GH-D z - Z. <g O 2 <C O X I A. Patent Application Publication Mar. 30, 2006 Sheet 2 of 50 US 2006/0068405 A1 N V S. 545 - Z CN y O O Ž- w seO M) Z.Sd CD O A. OD A. op Z. O <g O A 2. S Patent Application Publication Mar. 30, 2006 Sheet 3 of 50 US 2006/0068405 A1 Patent Application Publication Mar. 30, 2006 Sheet 4 of 50 US 2006/0068405 A1 O N ef a C9 s CD Op. s - Patent Application Publication Mar. 30, 2006 Sheet 5 of 50 US 2006/0068405 A1 Figure 4 1 tumor 1.1 epithelial cell tumors 1.1.1 carcinoma 1.1.1.1 adenocarcinoma 1.1.1.2 lobular carcinoma 1.2 Mesenchimal cell tumors 1.2.1 sarcoma 1.2.1.1 liposarcoma 1.2.1.2. rhabdomyosarcoma 1.2.1.3 pnet 1.2.1.4 ewing sarcoma 1.3 blood tumors 1.3.1 lymphoma 1.3.2 leukemia 1.3.3 myeloma 1.4 endocrine tumors 1.4.1 pheocromocytoma 1.4.2 carcinoid Patent Application Publication Mar. 30, 2006 Sheet 6 of 50 US 2006/0068405 A1 Figure 4 2 endocrine system 2.1 adrenal 2.1.1 pheocromocytoma 2.2 pancreas 2.2.1 islets of Langerhans 2.3 neuroendocrine 2.3.1 hypothalamus 2.3.2 carcinoid 2.4 thyroid 3 vascular tissue 3.1 arteries 3.1.1 aorta 3.2 Vein Patent Application Publication Mar. 30, 2006 Sheet 7 of 50 US 2006/0068405 A1 Figure 4 4 genitourinary System 4.1 urinary system 4.1.1 bladder 4.1.2 kidney 4.2 genital system 4.2.1 women genital system 4.2.1.1 cervix 4.2.1.2 ovary 4.2.1.3 uterus 4.2. I.3.I endometrium 4.2.2 men gentile system 4.2.2.1 prostate 4.2.2.2 testis 4.2.2.2.1 epididymis 5 muscles 5.1 rhabdomyosarcoma 5.2 tongue - 5.3 bladder 5.4 heart 5.5 uterus Patent Application Publication Mar. 30, 2006 Sheet 8 of 50 US 2006/0068405 A1 Figure 4 6 Blood 6.1 peripheral blood 6.1.1 erythroid line 6.1.2 leukocyte 6.1.2.1 lymphoid system 6. I.2.1. I lymphoma 6.1.2.1.2 spleen 6. I.2.1.3 thalamus 6.2 stem cells 6.2.1 myeloid 6.2.2 myeloma 6.3 'Bone narrow 6.4 leukemia Patent Application Publication Mar. 30, 2006 Sheet 9 of 50 US 2006/0068405 A1 Figure 4 7 nerve system 7.1 CNS, central nervous system 7.1.1 brain 7.1.1.1 cerebrum 7.1.1.2 cerebellum 7.1.1.3 pitituary gland 7.1.1.4 hypothalamus 7.1.1.5 thalamus 7.1.1.6 olfactory 7.1.1.7 Hippocampus 7.1.1.8 amygdala 7.1.1.9 frontal lobe 7.1.1.10 pnet 7.2 Embryonal nerve system 7.2.1 primitive neuroectoderm 7.3 retina 7.3.1 retinobastoma Patent Application Publication Mar. 30, 2006 Sheet 10 of 50 US 2006/0068405 A1 Figure 4 8 breast 8.1 ductal breast 8.1.1 ductal carcinoma 8.2 lobular carcinoma 8.3 mammary 9 skeleton 9.1 bone 9.1.1 evving sarcoma 9.1.2 craniofacial 9.1.2.1 cavarium 9.2 connective tissue 9.2.1 trabeculae 9.2.2 cartilage 10 embryo 10.1 annion . 10.2 chorion 10.3prinitive neuroectodern 10.4 placenta Patent Application Publication Mar. 30, 2006 Sheet 11 of 50 US 2006/0068405 A1 Figure 4 11 exocrine system 11.1 pancreas 11.1.1 islets of Langerhans 11.2prostate 11.3salivary gland Patent Application Publication Mar. 30, 2006 Sheet 12 of 50 US 2006/0068405 A1 Figure 4 12 face organs 12.1 nose 12.2ear 12.2.1 cochlea 12.3eye 12.3.1 retina 12.3.1.1 retinoblastoma 12.3.2 lens 12.4mouth 12.5 tongue 13 gastrointestinal system. 13.1 mucosa 13.2stomach 13.3 intestine 13.3.1 colorectal 13.3.1.1 colon 13.4 hepatobiliary system 1341 liver 13.4.2 biliary system 13.4.2.1 gallbladder 13.5 pancreas 13.5.1 islets of Langerhans Patent Application Publication Mar. 30, 2006 Sheet 13 of 50 US 2006/0068405 A1 Figure 4 14 respiratory system 14.1 nasopharynx 14.2 lung 14.2.1 : Small cell lung carcinoma 15 skin 15.1 dernis 15.1.1 melanocyte 16 fat tissue 16.1 liposarcoma Patent Application Publication Mar. 30, 2006 Sheet 14 of 50 US 2006/0068405 A1 separe th as A s h Figure 5 Patent Applicaication d Publicaication Mar. 30, 2006 Sheet 16 Of 5 O US 200 6/00684 05 A1 i . 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