Table 2. Expression data from DGE analysis of the 80 selected transcripts in whole-blood cells in IQ+ versus IQ− patients.
DGE-tag | IQ+ | IQ− | P-value | Sequence i.d. | Cyt loc | Hugo name | Description | GO annotation |
---|---|---|---|---|---|---|---|---|
5′-CAAATGAGGAGTGCCAG-3′ | 0 | 541 | 1E−160 | NM_001130523 | 1p13.2 | CSDE1 | Neuroblastoma RAS viral (v-ras) oncogene homolog | P:regulation of transcription, DNA-dependent |
5′-TCCAAAGTAATGGAGAT-3′ | 0 | 247 | 1E−72 | BC000301 | 1p34 | HDAC1 | Histone deacetylase 1 | F:histone deacetylase activity |
5′-ATCAGTGGCTTTGAATG-3′ | 0 | 239 | 3E−70 | BC000331 | 1q21 | PSMB4 | Proteasome (prosome, macropain) subunit, β-type 4 | P:small molecule metabolic process |
5′-GAAGCCCCAGCTCAGCT-3′ | 842 | 3 | 1E−124 | BC066343 | 2p12 | IGKC | Immunoglobulin κ-constant | P:regulation of immune response |
5′-ATATTTTAAATGTTAAG-3′ | 0 | 183 | 2E−53 | BC047933 | 2p15 | B3GNT2 | UDP-GlcNAc: β-Gal-β-1,3-N-acetylglucosaminyltransferase 2 | F:transferase activity, transferring glycosyl groups |
5′-TTCATACACCTATCCCC-3′ | 432 | 27556 | 3E−118 | BC001797 | 2p16.1 | CCDC104 | Coiled-coil domain-containing 104 | |
5′-TTAACAACATTAAAAAC-3′ | 22 | 64 | 2E−06 | NM_001139488 | 2p25.1-p24.1 | RASGRP3 | RAS guanyl releasing protein 3 (calcium and DAG-regulated) | F:Ras GTPase binding |
5′-TCATTGTAATGATTTCA-3′ | 0 | 237 | 1.46E−69 | BC014274 | 2q11.2 | STARD7 | StAR-related lipid transfer (START) domain containing 7 | |
5′-GAAAAATGGTTGATGGA-3′ | 0 | 4692 | 3E−174 | BC010054 | 3p22.2 | RPSA | Ribosomal protein SA | P:mRNA metabolic process |
5′-CGTGTTAATGGCTGTTC-3′ | 0 | 171 | 7E−50 | BC000288 | 3q21 | CNBP | CCHC-type zinc finger, nucleic acid-binding protein | P:positive regulation of transcription from RNA polymerase II promoter |
5′-TCTTAATGAAGTTTGAA-3′ | 0 | 286 | 3E−84 | CR612348 | 3q28 | EIF4A2 | Eukaryotic translation initiation factor 4A2 | F:helicase activity |
5′-ATGTCATCAAATGGGTG-3′ | 0 | 217 | 1E−63 | NM_004068 | 3q28 | AP2M1 | Adaptor-related protein complex 2, mu 1 subunit | P:intracellular protein transport |
5′-TGTGCTAAATGTGTTCG-3′ | 0 | 673 | 2E−200 | BC070208 | 4q25 | RPL34 | Ribosomal protein L34 | F:structural constituent of ribosome |
5′-ATACTTTAATCAGAAGC-3′ | 0 | 186 | 2E−54 | NM_001154 | 4q26-q28|4q27 | ANXA5 | Annexin A5 | F:receptor tyrosine kinase binding |
5′-TCTGCAATGAAGAGATT-3′ | 0 | 372 | 1E−109 | BC005288 | 5q13.3 | NSA2 | NSA2 ribosome biogenesis homolog (S. cerevisiae) | P:rRNA processing |
5′-TTACTAAATGGTGTTAC-3′ | 0 | 428 | 8E−127 | NM_001746 | 5q35 | CANX | Calnexin | P:protein secretion |
5′-ACACTAAAATGGCAGAG-3′ | 0 | 191 | 8E−56 | BC011676 | 6p21.1 | NFKBIE | Nuclear factor of κ-light polypeptide gene enhancer in B-cells inhibitor, epsilon | P:D-serine transport |
5′-TTGATTTCTTAGCTGAC-3′ | 425 | 1 | 6E−126 | AF533900 | 6p21.3 | HLA-DQA1 | Major histocompatibility complex, class II, DQ-α 1 | P:T-cell receptor-signaling pathway |
5′-GCAGTTCTGACAGTGAC-3′ | 1616 | 1 | 1E−119 | AK290388 | 6p21.3 | HLA-DRB1 | Major histocompatibility complex, class II, DR-β 1 | F:peptide antigen binding |
5′-TAGATAATGGCCATCAT-3′ | 0 | 372 | 5E−110 | AK098772 | 6p21.33 | TUBB | Tubulin-β | F:structural constituent of cytoskeleton |
5′-GTCTTAAAGTGAGATTT-3′ | 4 | 16 | 4E−03 | NM_000636 | 6q25.3 | SOD2 | Superoxide dismutase 2, mitochondrial | P:negative regulation of fat cell differentiation |
5′-TACATCCGAATGCTAAA-3′ | 0 | 212 | 4E−62 | NM_001128619 | 7q33 | LUZP6 | Myotrophin | P:positive regulation of macromolecule biosynthetic process |
5′-AACAGAAGCAAATGATG-3′ | 0 | 396 | 3E−117 | BG480804 | 8q13|8q13 | SNHG6 | Small nucleolar RNA host gene 6 (non-protein coding) | |
5′-ATCAAATGCAACCTCAC-3′ | 0 | 364 | 1E−107 | NM_002467 | 8q24.21 | MYC | V-myc myelocytomatosis viral oncogene homolog (avian) | F:sequence-specific DNA-binding transcription factor activity |
5′-GACAATGCCAGCAAGAA-3′ | 0 | 165 | 4E−48 | NM_001001973 | 10p15.1 | ATP5C1 | ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 | P:small molecule metabolic process |
5′-GCCATAAAATGGCTTTA-3′ | 0 | 745 | 5E−222 | NM_002727 | 10q22.1 | SRGN | Serglycin | P:mast cell secretory granule organization |
5′-CTAAATATTCTTTCCTA-3′ | 22 | 55 | 6E−05 | NM_005445 | 10q25 | SMC3 | Structural maintenance of chromosomes 3 | P:chromosome organization |
5′-GGGACGGCGCGGAGGAG-3′ | 29 | 51 | 4E−03 | NM_030930 | 11q13 | UNC93B1 | Unc-93 homolog B1 (C. elegans) | P:toll-like receptor-3 signaling pathway |
5′-GTACAGGCTTGGAGCTT-3′ | 85 | 32 | 3E−07 | NM_012296 | 11q14.1 | GAB2 | GRB2-associated binding protein 2 | P:phosphatidylinositol-mediated signaling |
5′-GACTTTTCTGGGAAATG-3′ | 0 | 179 | 3E−52 | Z49194 | 11q23.1 | POU2AF1 | POU class 2 associating factor 1 | P:regulation of transcription, DNA-dependent |
5′-AATAGGTCCAACCAGCT-3′ | 9081 | 577 | 5E−123 | NM_001028 | 11q23.3 | RPS25 | Ribosomal protein S25 | P:mRNA metabolic process |
5′-CCAGGAGGAATGCCTGG-3′ | 0 | 243 | 2E−71 | BC042163 | 11q24.1 | HSPA8 | Heat shock 70 kDa protein 8 | F:ATPase activity, coupled |
5′-TTTCTGTATGTTAATGA-3′ | 0 | 415 | 6E−123 | NM_001013699 | 12p11.21 | H3F3C | H3 histone, family 3C | F:DNA binding |
5′-GAAATGATGAGTCAGAA-3′ | 0 | 250 | 3E−73 | BM562920 | 12q12 | PFDN5 | Prefoldin subunit 5 | P:cellular protein metabolic process |
5′-GAAATGTAAGAGTGGAA-3′ | 0 | 357 | 1E−105 | AK123458 | 12q13.12-q13.13 | PCBP2 | Poly(rC)-binding protein 2 | F:RNA binding |
5′-GTGCTGAATGGCTGAGG-3′ | 0 | 1162 | 9E−173 | BC017455 | 12q13.2 | MYL6 | Myosin, light chain 6, alkali, smooth muscle and non-muscle | P:skeletal muscle tissue development |
5′-TCACAAGCAAATGTGTC-3′ | 0 | 5532 | 9E−206 | NM_001113203 | 12q23-q24.1 | NACA | Nascent polypeptide-associated complex-α subunit | P:translation |
5′-TTTCTGTGAAAATGTAT-3′ | 0 | 232 | 4E−68 | NM_004592 | 12q24.33 | SFSWAP | Splicing factor, suppressor of white-apricot homolog (Drosophila) | P:regulation of transcription, DNA-dependent |
5′-CTGTTGATTGCTAAATG-3′ | 0 | 334 | 1E−98 | AK126454 | 13q14.3 | HNRNPA1L2 | Heterogeneous nuclear ribonucleoprotein A1-like 2 | F:RNA binding |
5′-TCAAATGCATCCTCTAG-3′ | 0 | 702 | 4E−209 | AK126950 | 14q11.2 | HNRNPC | Heterogeneous nuclear ribonucleoprotein C (C1/C2) | F:nucleic acid binding |
5′-GAGATCCGCAATGCTTA-3′ | 0 | 745 | 5E−222 | NM_006263 | 14q11.2 | PSME1 | Proteasome (prosome, macropain) activator subunit 1 (PA28-α) | P:small molecule metabolic process |
5′-GAGATGCCTTTGGTGCT-3′ | 17 | 3 | 1E−03 | NM_005132 | 14q11.2-q12 | REC8 | REC8 homolog (yeast) | P:meiosis |
5′-GAAATAAAGCACCCACC-3′ | 8003 | 739 | 1E−96 | BC016381 | 14q32.33 | IGHM | Immunoglobulin heavy constant gamma 1 (G1m marker) | F:antigen binding |
5′-TTTAATACATAGGTGAT-3′ | 0 | 189 | 3E−55 | NM_001014812 | 15q22.31 | FAM96A | Family with sequence similarity 96, member A | F:molecular_function |
5′-TAATGGTAACTTGGACT-3′ | 0 | 177 | 1E−51 | NM_004255 | 15q24.1 | COX5A | Cytochrome c oxidase subunit Va | F:metal ion binding |
5′-TTTGTATTGCACAGATC-3′ | 29 | 49 | 6E−03 | NM_144572 | 15q24.3-q25.1 | TBC1D2B | TBC1 domain family, member 2B | F:phospholipid binding |
5′-AGACCTGTAATAAAATA-3′ | 6 | 20 | 3E−03 | NM_006565 | 16q21-q22.3 | CTCF | CCCTC-binding factor (zinc finger protein) | P:regulation of histone methylation |
5′-AAAAAGATAATGGAGAC-3′ | 0 | 215 | 5E−63 | AK295346 | 18q21.32 | SEC11C | SEC11 homolog C (S. cerevisiae) | P:cellular protein metabolic process |
5′-GCCTTATCTGTTCCAGT-3′ | 33 | 9 | 1E−04 | NM_002918 | 19p13.1 | RFX1 | Regulatory factor X, 1 (influences HLA class II expression) | F:RNA polymerase II distal enhancer sequence-specific DNA-binding transcription factor activity |
5′-TGTTAATGTTACGATGT-3′ | 0 | 243 | 2E−71 | AB209074 | 19p13.3 | MKNK2 | MAP kinase-interacting serine/threonine kinase 2 | F:protein serine/threonine kinase activity |
5′-CACGCAATGCTAGCTGC-3′ | 0 | 654 | 1E−194 | AK095154 | 19p13.3 | AES | Amino-terminal enhancer of split | P:response to interleukin-1 |
5′-CCCCCAATGCTGAGGCC-3′ | 0 | 684 | 1E−203 | NM_007165 | 19p13.3-p13.2 | SF3A2 | Splicing factor 3a, subunit 2, 66 kDa | F:metal ion binding |
5′-GCCCAGCTCAAATGCTA-3′ | 0 | 189 | 3E−55 | AK308809 | 19q13.2 | PSMD8 | Proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 | P:proteolysis |
5′-AAATGTTTGGCCTTAGT-3′ | 0 | 368 | 8E−109 | NM_012068 | 19q13.3 | ATF5 | Activating transcription factor 5 | F:sequence-specific DNA binding |
5′-CCTTCGAGATCATACAC-3′ | 147 | 5856 | 2E−189 | BG165682 | 19q13.4 | RPS5 | Ribosomal protein S5 | P:mRNA metabolic process |
5′-CCAGGAACAATGTCTCC-3′ | 0 | 309 | 4E−91 | AK054634 | 20p11 | SNX5 | Sorting nexin 5 | P:cell communication |
5′-ACAAATCCTTGAATGTT-3′ | 0 | 290 | 1E−85 | NM_000801 | 20p13 | FKBP1A | FK506-binding protein 1A, 12 kDa | F:transforming growth factor-β-activated receptor activity |
5′-AAGGAAGCAATGGTTCA-3′ | 0 | 163 | 3E−47 | NM_006392 | 20p13 | NOP56 | NOP56 ribonucleoprotein homolog (yeast) | F:RNA binding |
5′-TAAATAAATACATTCTT-3′ | 0 | 6 | 5E−03 | NM_000484 | 21q21.2 | APP | Amyloid-β (A4) precursor protein | P:axon cargo transport |
5′-GACTTGGCCCAAAAGAA-3′ | 64 | 5 | 1E−14 | NM_000819 | 21q22.11 | GART | Phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase | P:small molecule metabolic process |
5′-GCTTCCTAAATGGCCCT-3′ | 0 | 6 | 500E−03 | NM_000071 | 21q22.3 | CBS | Cystathionine-β-synthase | P:cartilage development involved in endochondral bone morphogenesis |
5′-CTCAGGAAATAAATGTG-3′ | 0 | 192 | 4E−56 | BC005402 | 22cen-q12.3 | UQCR10 | Ubiquinol-cytochrome c reductase, complex III subunit X | P:small molecule metabolic process |
5′-AACGCGGCCAATGTGGG-3′ | 0 | 623 | 4E−185 | BC036909 | 22q11.23 | LOC284889 | Hypothetical LOC284889 | F:phenylpyruvate tautomerase activity |
5′-AAACTAGAAATGTCATC-3′ | 0 | 433 | 2E−128 | AF230904 | Xp22.1-p21.3 | SH3KBP1 | SH3-domain kinase-binding protein 1 | P:regulation of cell shape |
5′-CAATGTGTTATGTAGTG-3′ | 0 | 197 | 1E−57 | NM_004541 | Xq24 | NDUFA1 | NADH dehydrogenase (ubiquinone) 1-α subcomplex, 1, 7.5 kDa | F:NADH dehydrogenase (ubiquinone) activity |
5′-GTTAATAACAAATGAAT-3′ | 0 | 35 | 2E−11 | NM_006603 | Xq25 | STAG2 | Stromal antigen 2 | P:negative regulation of DNA endoreduplication |
5′-TGAAGGATGCCAATGGC-3′ | 0 | 220 | 1E−64 | NM_001008 | Yp11.3 | RPS4Y1 | Ribosomal protein S4, Y-linked 1 | P:mRNA metabolic process |
5′-GAATCCAACTGCTTCGA-3′ | 3597 | 176 | 5E−105 | AJ712551 | — | — | Transcribed locus, moderately similar to NP_061929.2 NADH dehydrogenase (ubiquinone) 1-β subcomplex subunit 11, mitochondrial isoform 1 (Homo sapiens) | P:small molecule metabolic process |
5′-CTGCTATACGAGAGAAT-3′ | 22 | 2699 | 2E−192 | AV755966 | — | — | Transcribed locus, strongly similar to XP_003086526.1 PREDICTED: 60S ribosomal protein L5-like isoform 3 (Mus musculus) | P:mRNA metabolic process |
5′-AGGGCAGGGAATGTGTC-3′ | 0 | 175 | 4E−51 | AW967735 | — | — | Transcribed locus | |
5′-ACTTTTTCAAAAAAAAA-3′ | 5286 | 213 | 3E−159 | BE877281 | — | — | Transcribed locus, strongly similar to NP_001460.1 X-ray repair cross-complementing protein 6 (Homo sapiens) | F:helicase activity |
5′-GGGACGGCGCGGAGGAG-3′ | 29 | 51 | 4E−03 | BG469659 | — | — | Transcribed locus, moderately similar to XP_001721426.3 PREDICTED: protein unc-93 homolog B1-like (Homo sapiens) | P:toll-like receptor 3-signaling pathway |
5′-AATAAATGGATCTGTGA-3′ | 0 | 224 | 1E−65 | BG498681 | — | — | Transcribed locus, moderately similar to NP_004885.1 6.8 kDa mitochondrial proteolipid isoform 1 (Homo sapiens) | |
5′-CAAATGAGGAGTGCCAG-3′ | 0 | 541 | 1E−160 | BG680089 | — | — | Transcribed locus, strongly similar to XP_002729159.1 PREDICTED: cold shock domain-containing E1, RNA binding (Rattus norvegicus) | |
5′-TTTATTTAAGAAATGGA-3′ | 0 | 239 | 3E−70 | BM541359 | — | — | Transcribed locus, strongly similar to NP_001013208.1 UV excision repair protein RAD23 homolog A (Rattus norvegicus) | |
5′-CAATAAATGTTCTGGTT-3′ | 0 | 1496 | 6E−223 | BM553029 | — | — | CDNA clone IMAGE:6385453 | F:metal ion binding |
5′-TTTTTAATGTTGTCTGT-3′ | 0 | 233 | 2E−68 | BU566862 | — | — | Transcribed locus | |
5′-CTTCGGATGTCTTGGAG-3′ | 16 | 73 | 2E−10 | NM_001007226 | — | SPOP | Transcribed locus | F:ubiquitin protein ligase binding |
5′-CCACCCCGAATGGCTCA-3′ | 0 | 771 | 8E−230 | NM_001098576 | — | — | Transcribed locus | P:apoptotic process |
5′-AATACTTAAATGCCAAC-3′ | 0 | 399 | 4E−118 | NM_006990 | — | WASF2 | MRNA adjacent to 3- end of integrated HPV16 (INT290) | P:lamellipodium assembly |
The 17 bp DGE-tags are indicated in the first column. The 2nd and 3rd columns indicate the exact occurrences of the DGE-tags sequenced. The ‘0' value indicate that a DGE-tag was not identified in one of the 2 groups. Some GO (http://www.geneontology.org/) annotations are listed in the last column with ‘P:*' for Biological process and ‘F:*' for molecular function.