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TABLE 5. Proteins Identified in Cumulus and Oocyte. GI Number

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TABLE 5. Proteins identified in Cumulus and Oocyte. GI Cell Protein DDF Protein name Peptides number typea categoryb fraction 30523262 100 kDa coactivator C K 5 2 2852383 14-3-3 protein beta C K 2 4 2852385 14-3-3 protein gamma C K 14 4 298639 155 kda myosin light chain kinase homolog O K 1 1 576 17,000 dalton myosin light chain CO K 5 3 8118661 17-beta-hydroxysteroid dehydrogenase type 1 C K 2 3 17864970 17-beta-hydroxysteroid dehydrogenase type 1 CO K 38 3 59857747 1-acylglycerol-3-phosphate O-acyltransferase 4 O K 1 3 30017445 2',5'-oligoadenylate synthetase 1, 40/46kDa C K 2 4,3 66792906 2'-5' oligoadenylate synthetase 2 C K 1 1 7271506 2-amino-3-ketobutyrate coenzyme A ligase O K 2 1 31414871 2-enoyl thioester reductase C K 2 4,1 45219953 5-hydroxytryptamine receptor 2A C K 2 4,1 47564115 5-oxo-L-prolinase CO K 5 1 34392345 90-kDa heat shock protein beta CO K 54 1 56967054 A Chain A, Crystal Structure Of Bosus Mitochondrial Elongation Factor TuT O K 2 3 27807141 A disintegrin-like and metalloprotease (reprolysin type) with thrombos O K 1 3 89579 A23707 aminomethyltransferase (EC 2.1.2.10) precursor C K 3 3 89381 A29600 alkaline phosphatase (EC 3.1.3.1) precursor, hepatic - bovine O K 1 1 108687 A36623 gap junction protein Cx43 C K 3 4 89346 A40981 3',5'-cyclic-nucleotide phosphodiesterase (EC 3.1.4.17), cGMP-stimulated C K 1 4 1363022 A56351 cleavage and polyadenylation specificity factor 100K chain C K 1 3 1363051 A56534 interferon-induced double-stranded RNA-activated protein kinase inhibitor C K 1 4 14194421 AAKG1_BOVIN 5'-AMP-activated protein kinase, gamma-1 subunit C K 1 4 62751897 Abhydrolase domain containing 2 CO K 2 1 61554426 Abl-philin 2 isoform 2 CO K 2 3 63092048 Acetyl-CoA carboxylase, type beta C K 1 3 6006405 Acetyl-CoA-carboxylase C K 3 1 163596 Acid phosphatase C K 1 4 1649041 Acidic ribosomal phosphoprotein C K 2 1 2293577 Acidic ribosomal phosphoprotein PO C K 6 1 600177 Acidic ribosomal protein P2 C K 9 4 1351857 ACON_BOVIN Aconitate hydratase, mitochondrial precursor CO K 27 1 58013001 Actin [Cryptosporidium sp. ex Bosus] C K 5 4 61555662 Actin related protein 2/3 complex subunit 1B C K 1 2 27806765 Actin, beta CO K 20 2 1381584 Activin receptor type I C K 4 2 59857635 Acyl-Coenzyme A dehydrogenase, short/branched chain precursor C K 9 2 27806205 Acyl-coenzyme A dehydrogenase, very long chain C K 14 3 2498104 AD50_BOVIN ADRENAL MEDULLA 50 KD PROTEIN O K 1 2 20141178 ADA_BOVIN Adenosine deaminase (Adenosine aminohydrolase) O K 1 2 29420423 Adaptor related protein complex (AP)-3 delta subunit C K 2 4 57162630 Adaptor-related protein complex 3, mu 1 subunit C K 1 1 58760446 Adenine phosphoribosyltransferase C K 1 4 61888850 Adenylate kinase 1, soluble C K 1 4 217607 Adenylate kinase 2B CO K 18 1 895754 Adipocyte-type fatty acid binding protein C K 1 4 5823591 Adipophilin C K 2 3 13162341 ADP-ribosylation factor 2 C K 1 3 6680730 ADP-ribosylation factor-like 4 O K 1 1 3041655 ADRO_BOVIN NADPH:adrenodoxin oxidoreductase, mitochondrial precursor C K 3 4 52000728 ADT2_BOVIN ADP,ATP carrier protein 2 (ADP/ATP translocase 2) CO K 40 3 399012 ADT3_BOVIN ADP,ATP carrier protein, isoform T2 (ADP/ATP translocase 3) CO K 10 1 113469 ADX2_BOVIN Adrenodoxin 2, mitochondrial precursor (Adrenal ferredoxin) C K 1 4 31324244 Aggrecanase-1 OK 1 2 6319132 Aggrecanase-1 C K 1 4 6319134 Aggrecanase-2 C K 1 3 1352248 AL1A1_BOVIN Retinal dehydrogenase 1 (RalDH1) (RALDH 1) C K 1 4 162648 Albumin CO K 67 3 60302887 Aldose reductase C K 2 4 4097475 Allele: DQB*1004 C K 1 1 240434 Alpha 1C-adrenergic receptor [cattle, Peptide, 466 aa] C K 2 4,1 61553131 Alpha 2 actin CO K 69 2 386077 Alpha B-crystallin [cattle, lens, Peptide, 175 aa] C K 1 1 2967448 Alpha2(I) collagen C K 1 1 37652865 Alpha2,3-sialyltransferase O K 1 2 56292039 Alpha-2,6-sialyltransferase ST6Gal II C K 1 1 47564072 Alpha-2,8-sialyltransferase 8D C K 1 1 498822 Alpha-2-antiplasmin C K 1 3 61553826 Alpha-N-acetylgalactosaminidase precursor C K 2 4 2506821 AMBP_BOVIN AMBP protein precursor C K 1 4 525 Amine oxidase (flavin-containing); monoamine oxidase type A (MAO-A) C K 1 2 62751707 AminoadipateAminotransferase C K 1 2 4468135 Amyloid precursor protein O K 1 3 61555206 Amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate C K 1 2 20455472 ANG1_BOVIN Angiogenin-1 precursor O K 1 3 12643645 ANGP2_BOVIN Angiopoietin-2 (ANG-2) C K 1 1 61555439 Ankyrin repeatAnd SOCS box-containing protein 14 C K 1 2 59858367 Annexin 5 C K 15 4 61554010 Annexin A8 C K 3 4,1 61553085 Annexin I C K 2 3 1842109 Annexin VI C K 25 2 1168458 ANPRB_BOVIN Atrial natriuretic peptide receptor B precursor (ANP-B) C K 1 2 432627 Anti-testosteroneAntibody CO K 4 3 113956 ANXA4_BOVIN Annexin A4 (Annexin IV) (Lipocortin IV) (Endonexin I) C K 10 4 113983 APEX1_BOVIN DNA-(apurinic or apyrimidinic site) lyase (AP endonuclease 1) CO K 7 2 162678 Apolipoprotein A-I precursor CO K 7 1 46359698 Apolipoprotein C-III C K 2 3 162680 Apolipoprotein H O K 1 3 42564208 Apoliprotein A-I binding protein O K 3 1 47681470 Apoptosis inhibitor survivin C K 1 3 26453359 Apoptosis-associated speck-like protein containing a CARD C K 1 3 114151 ARBK1_BOVIN Beta-adrenergic receptor kinase 1 (Beta-ARK-1) C K 1 4 19354187 Arf3 protein C K 2 4 46213277 Argonaute 3 C K 1 3 162642 Aromatic-L-amino acid decarboxylase C K 2 4 50978894 ARP1 actin-related protein 1 homolog A, centractin alpha C K 1 1 3004445 Arylacetyl acyl-CoA N-acyltransferase C K 1 1 3492930 Arylacetyltransferase C K 6 1 33359641 Aryl-hydrocarbon receptor-interacting protein O K 1 2 59858077 Aspartate aminotransferase 1 C K 1 4 27807467 Aspartate beta-hydroxylase C K 3 1 60391782 ASPM_BOVIN Abnormal spindle-like microcephaly-associated protein homolog C K 1 4 114617 AT5F1_BOVIN ATP synthase B chain, mitochondrial C K 1 3 124013 ATIF1_BOVIN ATPase inhibitor, mitochondrial precursor CO K 3 3 114686 ATP5H_BOVIN ATP synthase D chain, mitochondrial CO K 12 1 231615 ATP5I_BOVIN ATP synthase e chain, mitochondrial CO K 2 3 114687 ATP5J_BOVIN ATP synthase coupling factor 6, mitochondrial precursor C K 1 3 19919710 ATPase 6 C K 2 3 27807317 ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member C K 1 3 61553266 ATPase, H+ transporting, lysosomal 31kD, V1 subunit E isoform 1 C K 3 2,1 14250784 ATPase, H+ transporting, lysosomal, V0 subunit D isoform 1 C K 2 3 114543 ATPB_BOVIN ATP synthase beta chain, mitochondrial precursor CO K 116 3 67010049 ATP-binding cassette sub-family A member 1 CO K 2 3 114579 ATPD_BOVIN ATP synthase delta chain, mitochondrial precursor C K 1 4 62751919 ATP-dependent Lon protease C K 2 4 22297308 Attractin C K 1 1 56967055 B Chain B, Crystal Structure Of Bosus Mitochondrial Elongation Factor O K 1 3 1083059 B54717 palmitoyl-protein thioesterase precursor C K 5 4 162731 Bactenecin 5 precursor C K 1 3 5442448 Band 3 protein C K 3 4 913808 Band 6 polypeptide B6P C K 1 3 33327729 Barrier-to-autointegration factor C K 7 2,1 2309001 BCNT C K 7 2 22779307 Bcnt C K 1 2 6224858 Beta actin CO K 30 3 312732 Beta prime cop C K 1 3 50844501 Beta tubulin CO K 42 3 61553937 Beta-1,3-N-acetylglucosaminyltransferase bGnT-6 O K 1 3 62177160 Beta-3-glucuronyltransferase P C K 1 4 62177158 Beta-3-glucuronyltransferase-S C K 1 3 25808793 Beta-actin binding proteinBetaCAP73 CO K 2 1 47523792 Beta-catenin C K 2 4 55416130 Beta-defensin 402 C K 2 4 2388780 Beta-nerve growth factor O K 1 3 7547262 Biglycan core protein precursor O K 1 3 685045 Bone sialoprotein; BSP C K 1 2 5705922 Bovine corneal protein 54; BCP 54 C K 1 3 3057087 Bovine submaxillary mucin 1 C K 2 2 285664 Bovine T cell receptor gamma chain C K 1 1 7715053 Bradykinin receptor B2 C K 1 4 1438984 Brain-type ribonuclease CO K 3 3 59858011 Branched chain aminotransferase 2, mitochondrial C K 1 1 13195201 BRCA1 C K 2 2,4 29640734 Breast and ovarian cancer susceptibility protein O K 1 3 1710369 BSP30 OK 1 3 27807233 Butyryl Coenzyme A synthetase 1 C K 1 4 30523021 Bv8/prokineticin 2-like protein CO K 2 3 46405153 C19orf10-like C K 1 4 453109 Ca(2+)-sensing receptor C K 1 3 27807135 Calcium channel, voltage-dependent, L type, alpha 1B subunit C K 1 4 2315159 Caldesmon OK 2 3 32766614 Calm2-prov protein C K 4 4 27806049 Calmodulin-dependent phosphodiesterase type 1 C K 1 4 27806721 Calpastatin C K 1 1 287744 CaMP-gated channel CO K 2 3 38322703 Capping protein (actin filament) muscle Z-line, alpha 2 C K 2 4 1838956 Capping protein, beta3 isoform C K 6 4 28192437 Carbonic anhydrase-related XI protein C K 1 1 59676559 CaSP8 and FADD-like apoptosis regulator C K 1 2 13924448 Catecholamine binding protein C K 1 3 1707415 Cathelicidin C K 1 3 809479 Cathepsin B C K 5 4 12697815 Cathepsin D CO K 4 2 59858409 Cathepsin L2 preproprotein C K 4 4 12803555 CBX1 protein C K 1 4 4928775 Cctq C K 5 2,4 56682913 CD2 antigen C K 1 4 27806911 CD9 antigen (p24) C K 1 3 19170724 CD97 protein OK 1 2 1345706 CDC2_BOVIN Cell division control protein 2 homolog (p34 protein kinase) O K 1 2 59857651 CDC37 homolog C K 1 4 61553589 Cdc42 guanine exchange factor 9 O K 1 3 59857983 CDC45-like C K 1 3 30794346 Cellular retinoic acid binding protein 1 C K 1 4 56182498 Cellular retinoic acid binding protein 2 C K 2 4 33323485 Cellular retinol binding protein 1 C K 5 4 32481980 C-Fos C K 1 1 37780029 CGI-105 protein C K 4 3 61554294 CGI-107 protein C K 1 4 59858441 CGI-30 protein OK 1 3 204 CGMP-gated channel C K 1 1 61553710 chaperonin containing TCP1, subunit 3 (gamma) C K 4 1 58760440 Chemokine (C-X-C motif) ligand 13-like C K 2 2 33415854 Chemokine receptor 7 C K 1 4 51316067 CHIA_BOVIN Acidic mammalian
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    Supplementary Table 1: Association of Gene Ontology Categories with Decay Rate for HepG2 Experiments These tables show details for all Gene Ontology categories. Inferences for manual classification scheme shown at the bottom. Those categories used in Figure 1A are highlighted in bold. Standard Deviations are shown in parentheses. P-values less than 1E-20 are indicated with a "0". Rate r (hour^-1) Half-life < 2hr. Decay % GO Number Category Name Probe Sets Group Non-Group Distribution p-value In-Group Non-Group Representation p-value GO:0006350 transcription 1523 0.221 (0.009) 0.127 (0.002) FASTER 0 13.1 (0.4) 4.5 (0.1) OVER 0 GO:0006351 transcription, DNA-dependent 1498 0.220 (0.009) 0.127 (0.002) FASTER 0 13.0 (0.4) 4.5 (0.1) OVER 0 GO:0006355 regulation of transcription, DNA-dependent 1163 0.230 (0.011) 0.128 (0.002) FASTER 5.00E-21 14.2 (0.5) 4.6 (0.1) OVER 0 GO:0006366 transcription from Pol II promoter 845 0.225 (0.012) 0.130 (0.002) FASTER 1.88E-14 13.0 (0.5) 4.8 (0.1) OVER 0 GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism3004 0.173 (0.006) 0.127 (0.002) FASTER 1.28E-12 8.4 (0.2) 4.5 (0.1) OVER 0 GO:0006357 regulation of transcription from Pol II promoter 487 0.231 (0.016) 0.132 (0.002) FASTER 6.05E-10 13.5 (0.6) 4.9 (0.1) OVER 0 GO:0008283 cell proliferation 625 0.189 (0.014) 0.132 (0.002) FASTER 1.95E-05 10.1 (0.6) 5.0 (0.1) OVER 1.50E-20 GO:0006513 monoubiquitination 36 0.305 (0.049) 0.134 (0.002) FASTER 2.69E-04 25.4 (4.4) 5.1 (0.1) OVER 2.04E-06 GO:0007050 cell cycle arrest 57 0.311 (0.054) 0.133 (0.002)
  • List of Down-Regulated Transcripts

    List of Down-Regulated Transcripts

    Supplementary Table 1: List of down-regulated transcripts (Fold Change>1.7 and p<0.05). List of the transcipts downregulated by Tpr-Met in P27 cachectic gastrocnemius muscles. Shown are the transcripts gene annotation: Mus Musculus Entrez Gene ID, official symbol from NCBI, average (AVG) Log2 Ratio derived from Illumina microarrays (3 replicates/condition), fold change and p-value computations, Log2 ratio over AVG Log2 controls and full definition of the genes. All genes modulated with a fold change > 1.7 and p-value<0.05 are included. AVG Entrez Gene Fold Symbol Log2 T-test Ctrl Ctrl Ctrl TM TM TM Definition ID Change Ratio - - - - 26908 Eif2s3y 3.598 12.1 0.000 0.146 0.248 0.102 3.712 3.571 -3.510 eukaryotic translation initiation factor 2, subunit 3, structural gene Y-linked (Eif2s3y), mRNA. - - - 13628 Eef1a2 1.333 2.5 0.011 -0.444 0.261 0.183 1.503 0.950 -1.546 eukaryotic translation elongation factor 1 alpha 2 (Eef1a2), mRNA. - - - 13628 Eef1a2 1.298 2.5 0.031 -0.383 0.275 0.108 1.632 0.605 -1.656 eukaryotic translation elongation factor 1 alpha 2 (Eef1a2), mRNA. - - - 56222 Cited4 1.268 2.4 0.029 -0.466 0.035 0.431 1.109 0.889 -1.805 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 4 (Cited4), mRNA. - - - 18810 Plec1 1.246 2.4 0.022 -0.440 0.327 0.113 1.303 0.779 -1.657 plectin 1 (Plec1), transcript variant 10, mRNA. - - - 20741 Spnb1 1.238 2.4 0.016 -0.384 0.314 0.071 1.129 0.902 -1.684 spectrin beta 1 (Spnb1), mRNA.
  • Effet De La Cryptorchidie Sur Le Transcriptome Testiculaire Humain

    Effet De La Cryptorchidie Sur Le Transcriptome Testiculaire Humain

    MARIE EVE BERGERON EFFET DE LA CRYPTORCHIDIE SUR LE TRANSCRIPTOME TESTICULAIRE HUMAIN Mémoire présenté à la Faculté des études supérieures et postdoctorales de l’Université Laval dans le cadre du programme de maîtrise en Physiologie-Endocrinologie pour l’obtention du grade de Maître ès sciences (M.Sc.) DÉPARTEMENT D’OBSTÉTRIQUE ET DE GYNÉCOLOGIE FACULTÉ DE MÉDECINE UNIVERSITÉ LAVAL QUÉBEC 2012 © Marie Eve Bergeron, 2012 Résumé Les niveaux d’expression de nombreux gènes peuvent être affectés par l’environnement et mener au développement de la cryptorchidie. Cette malformation congénitale est la plus commune dont une des conséquences majeures est l’infertilité masculine due au testicule non-descendu, auquel un risque plus élevé de cancer testiculaire est associé. L’expression des ARN totaux isolés à partir de biopsies testiculaires ont été analysés par micropuces, puis par une analyse bio-informatique et une validation par RT-qPCR de plusieurs gènes sélectionnés. Ces analyses m’ont permis d’identifier plus de deux milles candidats montrant une expression différente entre des sujets cryptorchides et normaux. Certains de ces gènes sélectionnés peuvent être associés à la descente testiculaire, d’autres au cancer testiculaire ou encore aux divers types cellulaires retrouvés dans cet organe. Les différences dans le transcriptome dues à la cryptorchidie vont nous aider à comprendre la cause génétique de cette maladie. ii Abstract Expression level of numerous genes may be affected by environmental condition and lead to development of cryptorchidism. The most common congenital malformation in male is cryptorchidism. One major consequence of this anomaly is infertility due to undescended testis, to which an increased risk of testicular cancer is associated.