TABLE 2.
mRNAs (160) enriched in the αCP2 immunoprecipitate relative to the control immunoprecipitate
| mRNA type and name | Probeset I.D.a | Accession no.b | Avg NFCc (INFCd) | Ranke |
|---|---|---|---|---|
| Splicing factors | ||||
| Spliceosomal protein (SAP62) | 37462_i_at | L21990 | 80 (57, 73, 96) | 1 |
| U1 snRNP-specific protein A | 40842_at | M60784 | 22 (12, 15, 45) | 14 |
| Spliceosomal protein (SAP49) | 33909_at | L35013 | 20 (9, 16, 42) | 20 |
| Splicing factor (SF3a120) | 34733_at | X85237 | 8 (4, 6, 17) | 117 |
| Enzymes | ||||
| Glutathione S-transferase subunit 4 | 39054_at | X08020 | 71 (27, 90, 118) | 2 |
| Pancreatic kallikrein | 246_at | M25629 | 29 (22, 28, 31) | 7 |
| Ubiquitin-conjugating enzyme 5B (UBCH5B) | 832_at | U39317 | 21 (12, 18, 32) | 18 |
| Na+, K+ ATPase beta 2 subunit | 37270_at | AF007876 | 18 (10, 14, 34) | 25 |
| Glutathione S-transferase M4 | 556_s_at | M96233 | 15 (9, 16, 21) | 37 |
| NADH-cytochrome B5 reductase | 36668_at | M28713 | 15 (6, 19, 24) | 39 |
| Lysosomal pepstatin-insensitive protease (CLN2) | 32824_at | AF039704 | 13 (7, 11, 24) | 54 |
| FK506-binding protein | 880_at | M34539 | 13 (8, 12, 17) | 59 |
| Vacuolar H+ ATPase proton channel subunit | 36994_at | M62762 | 12 (9, 10, 16) | 63 |
| Lysophosphatidic acid acyltransferase alpha | 32836_at | U56417 | 12 (6, 12, 20) | 68 |
| Palmitoyl-protein thioesterase 2 (PPT2) | 38108_at | AF020543 | 10 (4, 8, 20) | 103 |
| Pyruvate kinase L | 37077_at | D13243 | 9 (4, 7, 21) | 107 |
| Calcium ATPase (HK1) | 39791_at | M23114 | 7 (3, 6, 15) | 139 |
| 5-Aminolevulinate synthase (ALAS) | 37285_at | X60364 | 6 (3, 6, 9) | 154 |
| Cytoskeleton structure or motility | ||||
| Rho GDP-dissociation inhibitor 1 | 40164_at | X69550 | 47 (26, 55, 57) | 4 |
| Profilin | 36675_r_at | J03191 | 42 (15, 42, 90) | 6 |
| Dynamin | 32138_at | L07807 | 24 (14, 15, 55) | 9 |
| F-Actin capping protein beta subunit | 37012_at | U03271 | 18 (6, 21, 34) | 27 |
| EB3 | 40825_at | AB025186 | 17 (12, 18, 20) | 28 |
| Human serum constituent protein (MSE55) | 38132_at | M88338 | 15 (6, 19, 22) | 40 |
| Suppressor of yeast actin mutation 2 homologue | 32658_at | AL031228 | 13 (8, 12, 16) | 58 |
| Mutant β-actin (ACTB) | 32318_s_at | X63432 | 12 (4, 19, 20) | 67 |
| MacMarcks | 36174_at | X70326 | 11 (6, 11, 20) | 74 |
| BA46 (lactadherin) | 34403_at | U58516 | 11 (3, 10, 30) | 82 |
| Leukosialin (sialophorin) | 36798_g_at | J04168 | 10 (7, 8, 13) | 101 |
| Dematin 52-kDa subunit | 37192_at | U28389 | 9 (7, 8, 10) | 111 |
| Phospholipase D | 934_at | L11702 | 8 (5, 5, 17) | 128 |
| BAI-associated protein 2 alpha (BAP2-alpha) | 37760_at | AB015019 | 7 (4, 8, 10) | 134 |
| Mitochondrial enzymes | ||||
| Uncoupling protein homologue (UCPH) | 37591_at | U94592 | 27 (17, 25, 39) | 8 |
| Mitochondrial thioredoxin (Trx2) | 32852_at | U78678 | 13 (9, 10, 16) | 60 |
| Mitochondrial nucleoside-diphosphate kinase | 39089_at | Y07604 | 11 (6, 10, 18) | 78 |
| Outer membrane mitochondrial translocase | 37049_g_at | U58970 | 10 (5, 11, 12) | 97 |
| Citrate synthase | 41314_at | AF047042 | 7 (4, 5, 12) | 145 |
| NAD(H)-specific isocitrate dehydrogenase | 36574_at | Z68907 | 6 (4, 5, 8) | 151 |
| Transcription factors | ||||
| Mel-18 | 32192_g_at | D13969 | 24 (10, 30, 36) | 11 |
| T-cell factor 1, splice form C | 32649_at | X59871 | 21 (7, 17, 63) | 16 |
| Pleomorphic adenoma gene-like 1 (PLAGL1) | 36943_r_at | U81992 | 17 (11, 12, 26) | 30 |
| Homeodomain protein DLX-2 | 34585_at | L07919 | 15 (11, 14, 18) | 35 |
| Homeodomain protein HOXC6 | 40674_s_at | S82986 | 14 (9, 13, 21) | 46 |
| ROX protein | 35145_at | X96401 | 12 (7, 14, 16) | 61 |
| Upstream stimulatory factor 2 (USF2) | 39112_at | Y07661 | 12 (10, 10, 15) | 66 |
| High-mobility group protein (HMG-I(Y)) | 39704_s_at | L17131 | 12 (5, 15, 16) | 73 |
| JunD | 41483_s_at | X56681 | 8 (5, 5, 17) | 119 |
| NF-κB p65 subunit | 1295_at | L19067 | 8 (3, 9, 15) | 120 |
| NF-κB p65 subunit | 36645_at | L19067 | 8 (4, 10, 10) | 125 |
| Apolipoprotein AI regulatory protein (ARP-1) | 39397_at | M64497 | 8 (4, 6, 14) | 127 |
| RNA polymerase II largest subunit | 40791_at | X63564 | 7 (4, 5, 14) | 135 |
| T-cluster binding protein | 41763_g_at | D64015 | 7 (4, 6, 11) | 140 |
| G protein pathway suppressor 2 (GPS2) | 35653_at | U28963 | 6 (4, 6, 7) | 149 |
| Protein kinases | ||||
| c-src kinase | 1768_s_at | X59932 | 11 (7, 8, 18) | 77 |
| Casein kinase II (CKII) β-subunit | 410_s_at | X57152 | 10 (5, 12, 13) | 87 |
| A-Raf-1 kinase | 1706_at | U01337 | 10 (8, 9, 11) | 90/PICK> |
| Myt1 kinase | 480_at | U56816 | 10 (6, 8, 15) | 95 |
| MAP kinase kinase 5 (MEK5) | 513_at | U25265 | 10 (4, 10, 20) | 100 |
| Extracellular signal-regulated kinase 1 (ERK1) | 1000_at | X60188 | 9 (5, 10, 13) | 106 |
| Cell growth and proliferation | ||||
| KIP2 | 39903_at | AB012955 | 45 (22, 29, 110) | 5 |
| Insulin-like growth factor binding protein 4 | 39781_at | U20982 | 16 (11, 14, 22) | 32 |
| Thromboxane A2 receptor | 336_at | D38081 | 13 (9, 12, 16) | 55 |
| Insulin-like growth factor binding protein 4 | 1737_s_at | M62403 | 13 (6, 13, 20) | 57 |
| Neurite outgrowth-promoting protein | 38124_at | X55110 | 11 (5, 9, 26) | 75 |
| Calpain small subunit 1 (CAPNS1) | 36138_at | X04106 | 11 (8, 9, 13) | 84 |
| Epidermal growth factor response factor 1 | 38740_at | X79067 | 10 (5, 7, 26) | 85 |
| Midkine (MK) | 577_at | M94250 | 10 (4, 12, 17) | 89 |
| 14-3-3σ (stratifin) | 33323_r_at | X57348 | 10 (4, 11, 17) | 92 |
| 14-3-3ɛ | 1011_s_at | U54778 | 10 (5, 7, 22) | 96 |
| Phosphotyrosyl phosphatase 2A activator | 39127_f_at | X73478 | 10 (5, 11, 12) | 104 |
| Protein phosphatase 6 (PP6C) | 37581_at | X92972 | 8 (5, 5, 14) | 123 |
| Cyclin I | 1836_at | D50310 | 7 (5, 6, 8) | 142 |
| Connector enhancer of KSR-like protein (CNK1) | 38221_at | AF100153 | 5 (2, 4, 11) | 159 |
| Interferon-inducible factors | ||||
| Interferon-inducible gene I-8D | 411_i_at | X57351 | 22 (6, 33, 39) | 15 |
| Interferon-induced transmembrane protein 3 | 41745_at | X57352 | 10 (5, 13, 13) | 88 |
| Interferon-inducible protein 9-27 | 676_g_at | J04164 | 8 (7, 7, 9) | 118 |
| Polymeric immunoglobulin receptor | 34005_at | X73079 | 6 (4, 4, 10) | 156 |
| RNA binding proteins | ||||
| αCP-2 | 35746_r_at | X78136 | 12 (6, 12, 20) | 69 |
| αCP-2 | 35745_f_at | X78136 | 11 (6, 9, 17) | 83 |
| E1B 55 kDa-associated protein | 40106_at | AJ007509 | 9 (8, 8, 10) | 108 |
| Staufen | 41823_at | AJ132258 | 6 (4, 5, 9) | 152 |
| Poly(A) binding protein | 31950_at | Y00345 | 5 (2, 6, 7) | 160 |
| Other | ||||
| Alpha subunit of hemoglobin | 31525_s_at | J00153 | 53 (34, 48, 70) | 3 |
| Vacuolar ATPase 14-kDa subunit | 37395_at | D49400 | 22 (15, 21, 28) | 13 |
| Clone RP1-37E16 on chromosome 22 | 34046_at | z83844 | 20 (11, 13, 48) | 19 |
| Negative 14 gene | 40956_at | X90857 | 19 (10, 18, 28) | 23 |
| XE169 | 33268_at | L25270 | 18 (10, 12, 42) | 24 |
| Cosmid ICK0721Q.4.1 (PHD finger protein 2) | 40446_at | AL021366 | 15 (7, 20, 20) | 41 |
| Solute carrier family 7, member 8 (SLC7A8) | 41271_at | Y18483 | 15 (8, 15, 22) | 42 |
| Cleft lip and palate transmembrane protein | 41413_at | AF037339 | 15 (11, 14, 16) | 44 |
| Lymphocyte-secreted C-type lectin precursor | 37147_at | AF020044 | 14 (7, 12, 28) | 48 |
| TPRC gene | 39149_at | X99720 | 14 (11, 12, 16) | 49 |
| 28-kDa heat shock protein (hsp28) | 36785_at | Z23090 | 12 (6, 12, 20) | 62 |
| Amine oxidase pseudogene | 31626_i_at | AF047485 | 10 (4, 10, 24) | 86 |
| OXA1Hs | 39774_at | X80695 | 10 (5, 10, 17) | 93 |
| Homologue of yeast Rad23 protein A (hHR23A) | 41197_at | D21235 | 10 (6, 9, 14) | 94 |
| HSU93305 | 37326_at | U93305 | 10 (6, 10, 12) | 99 |
| OS-9 | 36996_at | U41635 | 10 (7, 10, 10) | 102 |
| Ras-related protein Rab5b | 37362_at | X54871 | 9 (6, 6, 17) | 112 |
| Clone C3 CHL 1 protein (CHLR1) | 31935_s_at | U75968 | 9 (4, 8, 14) | 114 |
| Major histocompatibility complex class I molecule | 35937_at | U65416 | 9 (4, 7, 20) | 115 |
| Na+/H+ exchanger 1 (NHE-1) | 32681_at | S68616 | 8 (4, 7, 13) | 124 |
| Clone 886K2 on chromosome 1p35.1-36.12 | 36986_at | AL031295 | 7 (4, 6, 14) | 133 |
| G protein coupled receptor (GPR19) | 156_s_at | U64871 | 7 (2, 7, 15) | 141 |
| G (i) protein alpha subunit | 37307_at | X04828 | 6 (4, 5, 10) | 147 |
| HLA-DMB | 41609_at | U15085 | 6 (4, 5, 10) | 148 |
| C1D protein | 39782_at | X95592 | 6 (2, 8, 10) | 155 |
| Unknown function | ||||
| 17b9 Homo sapiens cDNA | 32389_at | W25892 | 24 (18, 23, 28) | 10 |
| mRNA for hypothetical protein | 38483_at | AJ011916 | 24 (14, 21, 36) | 12 |
| ow26f02.x1 H. sapiens cDNA | 38663_at | AI033692 | 21 (14, 16, 32) | 17 |
| Ataxin-2 related protein | 34817_s_at | U70671 | 19 (9, 17, 36) | 21 |
| Homologue of yeast KDEL receptor | 37387_r_at | X55885 | 19 (9, 14, 42) | 22 |
| 43h8 H. sapiens cDNA | 39773_at | W28235 | 18 (15, 16, 20) | 26 |
| KIAA0048 gene | 37212_at | D28588 | 17 (9, 12, 36) | 29 |
| zh49e04.s1 H. sapiens cDNA | 38726_at | W80399 | 16 (12, 14, 20) | 31 |
| KIAA1100 gene | 41179_at | AB029023 | 16 (8, 11, 36) | 33 |
| wl90e10.x1 H. sapiens cDNA | 41047_at | AI885170 | 16 (12, 14, 19) | 34 |
| wf20e04.x1 H. sapiens cDNA | 40997_at | AI660963 | 15 (8, 11, 34) | 36 |
| DKFZp566K192_s1 H. sapiens cDNA | 32243_g_at | AL038340 | 15 (5, 19, 28) | 38 |
| KIAA0269 gene | 37190_at | D87459 | 15 (10, 11, 26) | 43 |
| af28f05.s1 H. sapiens cDNA | 38828_s_at | AA628946 | 14 (10, 12, 20) | 45 |
| zq95f07.s1 H. sapiens cDNA | 32163_f_at | AA216639 | 14 (12, 13, 14) | 47 |
| yx99b12.r1 H. sapiens cDNA | 38725_s_at | N36295 | 14 (10, 13, 16) | 50 |
| Glycophorin HeP2 | 41026_f_at | U05255 | 14 (8, 9, 26) | 51 |
| Myelodysplasia/myeloid leukemia factor 2 | 37719_at | AF070539 | 13 (7, 14, 20) | 52 |
| KIAA0909 protein | 41421_at | AB020716 | 13 (6, 18, 18) | 53 |
| KIAA0253 gene | 34835_at | D87442 | 13 (6, 14, 19) | 56 |
| Homologue of yeast KDEL receptor | 37386_i_at | X55885 | 12 (7, 9, 21) | 64 |
| Human clone 23722 mRNA sequence | 38093_at | U90909 | 12 (6, 10, 22) | 65 |
| Not 56-like protein | 38161_at | Y09022 | 12 (8, 12, 13) | 70 |
| Ki nuclear autoantigen | 39796_at | U11292 | 12 (6, 14, 15) | 71 |
| AF1q | 36941_at | U16954 | 12 (4, 14, 24) | 72 |
| DKFZp586H2219 H. sapiens cDNA | 39686_g_at | AL050282 | 11 (7, 7, 24) | 76 |
| hPMS3 | 31600_s_at | D38435 | 11 (8, 11, 12) | 79 |
| Putatively prenylated protein (CXX1) | 33856_at | Y13374 | 11 (7, 11, 14) | 80 |
| qy39a10.x1 H. sapiens cDNA | 39689_at | AI362017 | 11 (5, 6, 39) | 81 |
| Homologue of yeast NOT4 (NOT4H) | 32820_at | U71267 | 10 (7, 9, 12) | 91 |
| DKFZp564E242 H. sapiens cDNA | 38710_at | AL096714 | 10 (5, 11, 12) | 98 |
| mRNA expressed in placenta | 35308_at | D83200 | 10 (5, 10, 13) | 105 |
| zd37g06.r1 H. sapiens cDNA | 32736_at | W68830 | 9 (4, 7, 20) | 109 |
| yx76e06.s1 H. sapiens cDNA | 34329_at | N25547 | 9 (6, 9, 10) | 110 |
| KIAA0109 gene | 39795_at | D63475 | 9 (7, 8, 10) | 113 |
| qo77c11.x1 H. sapiens cDNA | 38705_at | AI310002 | 8 (5, 5, 18) | 116 |
| qb81g08.x1 H. sapiens cDNA | 37050_r_at | AI130910 | 8 (3, 10, 12) | 121 |
| KIAA0715 protein | 37415_at | AB018258 | 8 (3, 5, 24) | 122 |
| Leucine zipper protein | 39158_at | AB021663 | 8 (4, 6, 14) | 126 |
| af28f05.s1 H. sapiens cDNA | 38829_r_at | AA628946 | 8 (5, 7, 9) | 129 |
| zw93f01.r1 H. sapiens cDNA | 35805_at | AA447263 | 8 (5, 8, 8) | 130 |
| KIAA0544 protein | 32235_at | AB011116 | 7 (4, 8, 9) | 131 |
| DinG | 33484_at | Y10571 | 7 (4, 8, 10) | 132 |
| wh92e05.x1 H. sapiens cDNA | 32540_at | AI762547 | 7 (4, 5, 16) | 136 |
| KIAA1002 protein | 41366_at | AB023219 | 7 (5, 5, 11) | 137 |
| tu06g05.x1 H. sapiens cDNA | 39010_at | AI658639 | 7 (3, 7, 11) | 138 |
| Clone 24487 | 31961_r_at | AF070579 | 7 (3, 4, 17) | 143 |
| Clone 23704 | 35304_at | AF052130 | 7 (4, 5, 14) | 144 |
| KIAA0468 protein | 32092_at | AB007937 | 6 (4, 6, 8) | 146 |
| Synovial sarcoma (SS) X4 (SSX4) | 35950_at | U90841 | 6 (4, 5, 9) | 150 |
| KIAA0058 gene | 36616_at | D31767 | 6 (3, 6, 8) | 153 |
| Clone 24723 | 35328_at | AF055023 | 6 (3, 3, 16) | 157 |
| Clone 24448 | 34864_at | AF070638 | 5 (2, 6, 8) | 158 |
a
Affymetrix probeset identification number.
b
Genbank accession number.
c
Avg NFC using γ-globin as the normalization factor. This value reflects the relative enrichment of the mRNA species in the αCP2 immunoprecipitate relative to the control immunoprecipitate.
d
INFC for each independent microarray hybridization. Note that the average of these three values does not necessarily equal the Avg NFC because the normalization value used for the Avg NFC was an average of the normalization factor (γ-globin) from the three microarray hybridizations.
e
These rankings are based on the Avg NFC values.