Table 2.

Protein-Protein Interaction Pairs Identified in the High-Throughput in vivo Assay

PPI No. BIND clone ID annotation ACT clone ID annotation
10610006G13(J04716) ferritin light chain [M]0610006G13(J04716) ferrin light chain [M]
20610006G13(J04716) ferritin light chain [M]1500001P18(J03941) ferritin heavy chain [M]
30610007F07(K01515) hypoxanthine phosphoribosyltransferase [M]0610007F07(K01515) hypoxanthine phosphoribosyltransferase [M]
40610007L03(U46837) SRB7 [H]2010309C18(U94662) TFG protein [M]
50610007L13(X13752) delta-aminolevulinate dehydratase (AA 1-330) [M]0610007L13(X13752) delta-aminolevulinate dehydratase [M]
60610009D16(D14811) hypothetical protein KIAA0110 [H] e-1192410002G23(U96131) HPV16 E1 protein binding protein [H]
70610009O09(M13955) type II mesothelial keratin K7 [H]1200007G13(U13921) cytokeratin 13 [M]
80610009O09(M13955) type II mesothelial keratin K7 [H]2210407G07(AB013608) cytokeratin 17 [M]
90610009O09(M13955) type II mesothelial keratin K7 [H]4631426H08(AB013607) c29 [M] e-165
100610010C03(M28723) antioxidant protein 1 [M]0610010C03(M28723) antioxidant protein 1 [M]
110610010F19(AB013360) DPM2 [M]130015L18(AF050157) MHC class II beta chain [M]
120610011M09(AL049610) transcription elongation factor A (SII)-like 1 [H]1700023B02(AF098297) CBF1 interacting corepressor CIR [H]
130610012G03novel protein0610009O08(U24223) alpha-complex proein 1 [H]
140610012H09(M36429) transducin beta-2 subunit [H]0610009O08(U24223) alpha-complex protein 1 [H]
150610012K15(AF043225) 6-pyruvoyl-tetrahydropterin synthase [M]0610012K15(AF043225) 6-pyruvoyl-tetrahydropterin synthase [M]
160610027F08(AL023859) putative tRNA splicing endonuclease γ subunit [Sc] 9e-12110001K11(M81086) beta-tropomyosin [M]
170610030M18(AF022813) tetraspan [H]1500006F05(U19582) claudin-11 [M]
180610037N03(D63902) estrogen-responsive finger protein [M] 7e-102010309C18(U94662) TFG protein [M]
190610042A16(AF068179) calcium modulating cyclophilin ligand CAMLG [H]2010107G23novel protein
200610042H17(Z67995) pyrroline-5-carboxylate reductase [C] 1e-640610042H17(Z67995) pyrroline-5-carboxylate reductase [C] 1e-64
210910001B06(AF182293) U6 snRNA-associated Sm-like protein LSm7 [H]2310034K10(AJ238097) Lsm5 protein [H]
220910001F03(AF151884) CGI-126 protein [H]311001N19(AC000098) Similar to unknown protein [C] e-105
231010001P06(AF047659) No definition line found [C] 9e-922010323J02(U49112) ALG-2 [M]
241020013A21(D87438) Similar to a C. elegans protein [H]2310069P03(AC004839) similar to AL031532[H]
251100001A17(D28557) RYB-a [R]0610042H17(Z67995) pyrroline-5-carboxylate reductase [C] 1e-64
261110001H08(M59293) Id2 protein [M]3300001C01(U16321) MITF-2A protein [M]
271110001H08(M69293) Id2 protein [M]5730435I22(X54549) Pan-2 [R]
281110003H09(Z96932) nuclear autoantigen of 14 kDa [H]1110003H09(Z96932) nuclear autoantigen of 14 kDa [H]
291110004E04 novel protein1110004E04novel protein
301110004E04novel protein1110018O07novel protein
311110008E06novel protein2010309C18(U94662) TFG protein [M]
321110013A16(AF063937) squamous cell carcinoma antigen 2 [M]2900011O08(U95740) Unknown gene product [H]
331110014J03(AL110500) hypothetical protein [C]2310047L21(AC006465) supported by mouse EST AA277724 [H] 6e-31
341110020E15novel protein1810038N03novel protein
351110033F04(X80035) hair keratin associated protein [O] 5e-061110004E04novel protein
361110033F04(X80035) hair keratin associated protein [O] 5e-061110018O07novel protein
371110054P19novel protein1110004E04novel protein
381110054P19novel protein1110007B04novel protein
391190002C06novel protein1190002C06novel protein
401200005I04(AF095193) BAG-family molecualr chaperone regulator-3; BAG-3 [H]1300018P04(AF133207) protein kinase [H]
411200007G13(U13921) cytokeratin 13 [M]0610009O09(M13955) type II mesothelial keratin K7 [H]
421200015A19novel protein1200015A19novel protein
431300007C18(U66900) acid labile subunit [M]2010323J02(U49112) ALG-2 [M]
441300008O09novel protein0610012K15(AF043225) 6-pyruvoyl-tetrahydropterin synthase [M]
451500001L03novel protein0610012K15(AF043225) 6-pyruvoyl-tetrahydropterin synthase [M]
461500001P18(J03941) ferritin heavy chain [M]0610006G13(J04716) ferritin light chain [M]
471500001P18(J03941) ferritin heavy chain [M]1500001P18(J03941) ferritin heavy chain [M]
481500003N18(AF061346) Edp 1 protein [M] e-1031500003N18(AF061346) Edp 1 protein [M] e-103
491500006O17(J04716) ferritin light chain [M]1500031L05(AF026465) putative cell adhesion molecule [M]
501500012F11(AF074723) RNA polymerase transcriptional regulation mediator [H]1200015A19novel protein
511500016H19(AB001740) p27 [H]1500016H19(AB001740) p27 [H]
521500016H19(AB001740) p27 [H]2700002C15(Z31399) CCTeta protein eta chain [M]
531500037O10(U28068) neurogenic differentiation factor (neuroD) [M]3300001C01(U16321) MITF-2A protein [M]
541500040C19(X93357) SYT [M]0610043D20(Z85979) histone H3.3A [M]
551600014M03(U06755) acidic calponin [R]2310007K12(D37837) 65-kDa macrophage protein [M]
561700003P11(AF151883) CGI-125 protein [H]1110001O11(AF119676) RAB25 [M]
571700022I15(X75959) polyA binding protein [M]1700021C22(NM_011517) synaptonemal complex protein 3 [M]
581700025D04(U81002) TRAF4 associated factor 1 [H] 2e-742310047M10novel protein
591700026B03(L32752) GTPase (Ran) [M]2400006H24(Z49574) ORF YJR074w [Sc] 1e-10
601700029P02(AF019926) protein kinase [M]2010309C18(U94662) TFG protein [M]
621810014B23(X63469) TFIIE-beta [H]2810048P05novel protein
651810043E06(M60523) Id3 protein [M]3300001C01(U16321) MTF-2A protein [M]
661810043E06(M60523) Id3 protein [M]3110001I23(D32007) CBFA2T1(Mtg8a) [M]
722010016A14(U43884) Id1B protein [M]3110001I23(D32007) CBFA2T1(Mtg8a) [M]
732010016A14(U43884) Id1B protein [M]3300001C01(U16321) MITF-2A protein [M]
742010016A14(U43884) Id1B protein [M]5730435I22(X54549) Pan-2 [R]
852210407G07(AB013608) cytokeratin 17 [M]0610009O09(M13955) type II mesothelial keratin K7 [H]
912310015J09(M27734) keratin type I [M]330001P10(M19723) keratin K5 [H]
1192610027O10(AF029753) basic helix-loop-helix factor Cor1 [M]5730435I22(X54549) Pan-2 [R]
1332900002E16(D83999) RNA polymerase II 3 (Rpo2-3) [M]2810048P05novel protein
1413300001C01(U16321) MITF-2A proein [M]1110001H08(M69293) Id2 protein [M]

[i] Clone IDs and annotations of the participants in part of 145 interaction pairs are shown. The complete table is available as an on-line supplement at http://www.genome.org/ and also available at our Web site, http://genome.gsc.riken.go.jp/. Results ofBLASTX (2.0.11) search were used for the annotation. Where similar genes with an E-value of <e-5 are specified, their accession number in parenthesis, gene name, species (in brackets), and E-value are shown. In the case of identical or orthlogous genes, their E-values are omitted. Other clones are described as novel proteins.

[ii] Abbreviations of species are as follows: A, Arabidopsis thaliana; C, Caenorhabditis elegans; G, Gallus gallus; H, Homo sapiens; M, Mus musculus; Mt, Mycobacterium tuberculosis; O, Oryctolagus cuniculus; R, Rattus norvegicus; Sc,Saccharomyces cerevisiae; Sp, Schizosaccharomyces pombe; X, Xenopus laevis.

[iii] All interaction data in this report have been submitted to the public database BIND (http://www.bind.ca/).