DOCSLIB.ORG

556 Positive Significant Genes Computed Quantities Input

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Significant Genes List Input Parameters Imputation Engine Data Type Data in log scale? Number of Permutations Blocked Permutation? RNG Seed (Delta, Fold Change) (Upper Cutoff, Lower Cutoff) Computed Quantities Computed Exchangeability Factor S0 S0 percentile False Significant Number (Median, 90 percentile) False Discovery Rate (Median, 90 percentile) Pi0Hat 556 Positive Significant Genes Row Gene Name 5288 AGI_HUM1_OLIGO_A_23_P170096 6496 AGI_HUM1_OLIGO_A_23_P210021 9658 AGI_HUM1_OLIGO_A_23_P43444 9730 AGI_HUM1_OLIGO_A_23_P44466 12489 AGI_HUM1_OLIGO_A_23_P81507 666 AGI_HUM1_OLIGO_A_23_P108599 2085 AGI_HUM1_OLIGO_A_23_P127727 8831 AGI_HUM1_OLIGO_A_23_P32499 2483 AGI_HUM1_OLIGO_A_23_P132736 5424 AGI_HUM1_OLIGO_A_23_P17808 11383 AGI_HUM1_OLIGO_A_23_P66543 8456 AGI_HUM1_OLIGO_A_23_P2762 5455 AGI_HUM1_OLIGO_A_23_P1823 11724 AGI_HUM1_OLIGO_A_23_P71067 692 AGI_HUM1_OLIGO_A_23_P108932 4216 AGI_HUM1_OLIGO_A_23_P155504 13553 AGI_HUM1_OLIGO_A_23_P96529 5370 AGI_HUM1_OLIGO_A_23_P171284 10443 AGI_HUM1_OLIGO_A_23_P53946 5573 AGI_HUM1_OLIGO_A_23_P1981 3624 AGI_HUM1_OLIGO_A_23_P147869 9215 AGI_HUM1_OLIGO_A_23_P3766 10396 AGI_HUM1_OLIGO_A_23_P53257 9179 AGI_HUM1_OLIGO_A_23_P37251 8146 AGI_HUM1_OLIGO_A_23_P257762 6728 AGI_HUM1_OLIGO_A_23_P212720 6322 AGI_HUM1_OLIGO_A_23_P208059 6707 AGI_HUM1_OLIGO_A_23_P212499 12483 AGI_HUM1_OLIGO_A_23_P8142 7995 AGI_HUM1_OLIGO_A_23_P255925 6898 AGI_HUM1_OLIGO_A_23_P214681 8593 AGI_HUM1_OLIGO_A_23_P29472 8259 AGI_HUM1_OLIGO_A_23_P259192 13318 AGI_HUM1_OLIGO_A_23_P93015 10290 AGI_HUM1_OLIGO_A_23_P51861 9965 AGI_HUM1_OLIGO_A_23_P47709 4543 AGI_HUM1_OLIGO_A_23_P160226 5386 AGI_HUM1_OLIGO_A_23_P17269 10631 AGI_HUM1_OLIGO_A_23_P56356 13226 AGI_HUM1_OLIGO_A_23_P91850 6678 AGI_HUM1_OLIGO_A_23_P212179 10384 AGI_HUM1_OLIGO_A_23_P53137 3883 AGI_HUM1_OLIGO_A_23_P151415 2427 AGI_HUM1_OLIGO_A_23_P13202 9254 AGI_HUM1_OLIGO_A_23_P381261 3093 AGI_HUM1_OLIGO_A_23_P140967 328 AGI_HUM1_OLIGO_A_23_P104071 1579 AGI_HUM1_OLIGO_A_23_P120998 6464 AGI_HUM1_OLIGO_A_23_P209652 3845 AGI_HUM1_OLIGO_A_23_P150910 7852 AGI_HUM1_OLIGO_A_23_P25403 245 AGI_HUM1_OLIGO_A_23_P103091 3506 AGI_HUM1_OLIGO_A_23_P146325 9787 AGI_HUM1_OLIGO_A_23_P45409 5486 AGI_HUM1_OLIGO_A_23_P18656 1712 AGI_HUM1_OLIGO_A_23_P122717 3704 AGI_HUM1_OLIGO_A_23_P149042 11943 AGI_HUM1_OLIGO_A_23_P74264 5412 AGI_HUM1_OLIGO_A_23_P17642 7096 AGI_HUM1_OLIGO_A_23_P217009 6735 AGI_HUM1_OLIGO_A_23_P21282 11082 AGI_HUM1_OLIGO_A_23_P62684 687 AGI_HUM1_OLIGO_A_23_P108851 7271 AGI_HUM1_OLIGO_A_23_P218905 5223 AGI_HUM1_OLIGO_A_23_P169039 4836 AGI_HUM1_OLIGO_A_23_P164 8528 AGI_HUM1_OLIGO_A_23_P28614 7438 AGI_HUM1_OLIGO_A_23_P23850 6502 AGI_HUM1_OLIGO_A_23_P210082 4449 AGI_HUM1_OLIGO_A_23_P158771 3669 AGI_HUM1_OLIGO_A_23_P148519 1222 AGI_HUM1_OLIGO_A_23_P116435 6103 AGI_HUM1_OLIGO_A_23_P205662 4967 AGI_HUM1_OLIGO_A_23_P165703 3619 AGI_HUM1_OLIGO_A_23_P147805 11574 AGI_HUM1_OLIGO_A_23_P69179 13693 AGI_HUM1_OLIGO_A_23_P9831 8828 AGI_HUM1_OLIGO_A_23_P32454 6469 AGI_HUM1_OLIGO_A_23_P209700 449 AGI_HUM1_OLIGO_A_23_P10571 9789 AGI_HUM1_OLIGO_A_23_P45436 1447 AGI_HUM1_OLIGO_A_23_P119448 2952 AGI_HUM1_OLIGO_A_23_P139147 5217 AGI_HUM1_OLIGO_A_23_P168972 9884 AGI_HUM1_OLIGO_A_23_P46725 494 AGI_HUM1_OLIGO_A_23_P106412 12747 AGI_HUM1_OLIGO_A_23_P85519 10821 AGI_HUM1_OLIGO_A_23_P58960 9612 AGI_HUM1_OLIGO_A_23_P4286 6960 AGI_HUM1_OLIGO_A_23_P215377 6479 AGI_HUM1_OLIGO_A_23_P209805 5052 AGI_HUM1_OLIGO_A_23_P166777 9761 AGI_HUM1_OLIGO_A_23_P45025 3371 AGI_HUM1_OLIGO_A_23_P14454 13581 AGI_HUM1_OLIGO_A_23_P96976 8387 AGI_HUM1_OLIGO_A_23_P26863 270 AGI_HUM1_OLIGO_A_23_P103405 1535 AGI_HUM1_OLIGO_A_23_P120529 625 AGI_HUM1_OLIGO_A_23_P108124 7562 AGI_HUM1_OLIGO_A_23_P250412 2785 AGI_HUM1_OLIGO_A_23_P136843 6470 AGI_HUM1_OLIGO_A_23_P209712 1214 AGI_HUM1_OLIGO_A_23_P11633 10 AGI_HUM1_OLIGO_A_23_P201227 11638 AGI_HUM1_OLIGO_A_23_P70069 8131 AGI_HUM1_OLIGO_A_23_P257581 13513 AGI_HUM1_OLIGO_A_23_P95929 4022 AGI_HUM1_OLIGO_A_23_P153084 3747 AGI_HUM1_OLIGO_A_23_P149613 1379 AGI_HUM1_OLIGO_A_23_P118509 1005 AGI_HUM1_OLIGO_A_23_P113263 640 AGI_HUM1_OLIGO_A_23_P1083 11850 AGI_HUM1_OLIGO_A_23_P72897 13206 AGI_HUM1_OLIGO_A_23_P91583 12350 AGI_HUM1_OLIGO_A_23_P79591 3836 AGI_HUM1_OLIGO_A_23_P150804 1705 AGI_HUM1_OLIGO_A_23_P122617 1842 AGI_HUM1_OLIGO_A_23_P124384 13749 AGI_HUM1_OLIGO_A_23_P99044 1112 AGI_HUM1_OLIGO_A_23_P114903 5687 AGI_HUM1_OLIGO_A_23_P201071 13182 AGI_HUM1_OLIGO_A_23_P91212 137 AGI_HUM1_OLIGO_A_23_P101580 10481 AGI_HUM1_OLIGO_A_23_P54447 13727 AGI_HUM1_OLIGO_A_23_P9883 4652 AGI_HUM1_OLIGO_A_23_P161616 6102 AGI_HUM1_OLIGO_A_23_P205659 1047 AGI_HUM1_OLIGO_A_23_P11390 10968 AGI_HUM1_OLIGO_A_23_P60793 13588 AGI_HUM1_OLIGO_A_23_P97109 985 AGI_HUM1_OLIGO_A_23_P112974 4451 AGI_HUM1_OLIGO_A_23_P158794 5440 AGI_HUM1_OLIGO_A_23_P18055 7252 AGI_HUM1_OLIGO_A_23_P218681 2975 AGI_HUM1_OLIGO_A_23_P139442 283 AGI_HUM1_OLIGO_A_23_P103561 1947 AGI_HUM1_OLIGO_A_23_P126013 8060 AGI_HUM1_OLIGO_A_23_P256750 10819 AGI_HUM1_OLIGO_A_23_P58937 2386 AGI_HUM1_OLIGO_A_23_P131534 2593 AGI_HUM1_OLIGO_A_23_P134204 5071 AGI_HUM1_OLIGO_A_23_P167017 10817 AGI_HUM1_OLIGO_A_23_P58921 13396 AGI_HUM1_OLIGO_A_23_P94133 11353 AGI_HUM1_OLIGO_A_23_P66190 2538 AGI_HUM1_OLIGO_A_23_P133386 12814 AGI_HUM1_OLIGO_A_23_P86390 5150 AGI_HUM1_OLIGO_A_23_P16809 7325 AGI_HUM1_OLIGO_A_23_P22352 7475 AGI_HUM1_OLIGO_A_23_P2431 932 AGI_HUM1_OLIGO_A_23_P112241 10057 AGI_HUM1_OLIGO_A_23_P48868 4923 AGI_HUM1_OLIGO_A_23_P165136 7046 AGI_HUM1_OLIGO_A_23_P216412 11303 AGI_HUM1_OLIGO_A_23_P65609 4185 AGI_HUM1_OLIGO_A_23_P155079 11107 AGI_HUM1_OLIGO_A_23_P62999 11651 AGI_HUM1_OLIGO_A_23_P70258 6490 AGI_HUM1_OLIGO_A_23_P20995 12246 AGI_HUM1_OLIGO_A_23_P78209 13851 AGI_HUM1_OLIGO_A_32_P140898 2576 AGI_HUM1_OLIGO_A_23_P133974 6977 AGI_HUM1_OLIGO_A_23_P215580 1266 AGI_HUM1_OLIGO_A_23_P117052 9653 AGI_HUM1_OLIGO_A_23_P43380 7591 AGI_HUM1_OLIGO_A_23_P250824 3330 AGI_HUM1_OLIGO_A_23_P144067 11667 AGI_HUM1_OLIGO_A_23_P70454 2347 AGI_HUM1_OLIGO_A_23_P131074 12946 AGI_HUM1_OLIGO_A_23_P88179 6742 AGI_HUM1_OLIGO_A_23_P212914 2625 AGI_HUM1_OLIGO_A_23_P134653 4476 AGI_HUM1_OLIGO_A_23_P159190 10865 AGI_HUM1_OLIGO_A_23_P59447 6155 AGI_HUM1_OLIGO_A_23_P20622 867 AGI_HUM1_OLIGO_A_23_P111343 2053 AGI_HUM1_OLIGO_A_23_P127385 10497 AGI_HUM1_OLIGO_A_23_P5464 6832 AGI_HUM1_OLIGO_A_23_P213944 9923 AGI_HUM1_OLIGO_A_23_P47199 9977 AGI_HUM1_OLIGO_A_23_P47867 4521 AGI_HUM1_OLIGO_A_23_P159893 7297 AGI_HUM1_OLIGO_A_23_P21975 7512 AGI_HUM1_OLIGO_A_23_P24796 12175 AGI_HUM1_OLIGO_A_23_P77389 1832 AGI_HUM1_OLIGO_A_23_P124202 11213 AGI_HUM1_OLIGO_A_23_P64399 7493 AGI_HUM1_OLIGO_A_23_P24557 12647 AGI_HUM1_OLIGO_A_23_P83749 6925 AGI_HUM1_OLIGO_A_23_P215017 7599 AGI_HUM1_OLIGO_A_23_P250951 13584 AGI_HUM1_OLIGO_A_23_P97021 12513 AGI_HUM1_OLIGO_A_23_P81922 5290 AGI_HUM1_OLIGO_A_23_P170139 12623 AGI_HUM1_OLIGO_A_23_P83426 7079 AGI_HUM1_OLIGO_A_23_P216772 7644 AGI_HUM1_OLIGO_A_23_P251469 6095 AGI_HUM1_OLIGO_A_23_P205575 13781 AGI_HUM1_OLIGO_A_23_P99461 13535 AGI_HUM1_OLIGO_A_23_P96271 5726 AGI_HUM1_OLIGO_A_23_P201565 433 AGI_HUM1_OLIGO_A_23_P10548 5233 AGI_HUM1_OLIGO_A_23_P169133 5170 AGI_HUM1_OLIGO_A_23_P168410 216 AGI_HUM1_OLIGO_A_23_P102681 4220 AGI_HUM1_OLIGO_A_23_P155582 9663 AGI_HUM1_OLIGO_A_23_P4353 5933 AGI_HUM1_OLIGO_A_23_P203833 5957 AGI_HUM1_OLIGO_A_23_P204079 10922 AGI_HUM1_OLIGO_A_23_P60189 7031 AGI_HUM1_OLIGO_A_23_P216236 4251 AGI_HUM1_OLIGO_A_23_P156036 481 AGI_HUM1_OLIGO_A_23_P106162 11222 AGI_HUM1_OLIGO_A_23_P64538 11218 AGI_HUM1_OLIGO_A_23_P64482 1884 AGI_HUM1_OLIGO_A_23_P125025 7865 AGI_HUM1_OLIGO_A_23_P254214 10793 AGI_HUM1_OLIGO_A_23_P58588 9673 AGI_HUM1_OLIGO_A_23_P43663 9322 AGI_HUM1_OLIGO_A_23_P3911 5663 AGI_HUM1_OLIGO_A_23_P200801 1882 AGI_HUM1_OLIGO_A_23_P125011 3789 AGI_HUM1_OLIGO_A_23_P15018 3076 AGI_HUM1_OLIGO_A_23_P140748 9799 AGI_HUM1_OLIGO_A_23_P4561 10086 AGI_HUM1_OLIGO_A_23_P49230 2680 AGI_HUM1_OLIGO_A_23_P135315 4661 AGI_HUM1_OLIGO_A_23_P161727 12677 AGI_HUM1_OLIGO_A_23_P84268 12011 AGI_HUM1_OLIGO_A_23_P75260 4607 AGI_HUM1_OLIGO_A_23_P161049 6709 AGI_HUM1_OLIGO_A_23_P212515 10243 AGI_HUM1_OLIGO_A_23_P51253 6614 AGI_HUM1_OLIGO_A_23_P211360 1594 AGI_HUM1_OLIGO_A_23_P121179 3849 AGI_HUM1_OLIGO_A_23_P150960 13077 AGI_HUM1_OLIGO_A_23_P89851 6454 AGI_HUM1_OLIGO_A_23_P209544 2036 AGI_HUM1_OLIGO_A_23_P127167 4666 AGI_HUM1_OLIGO_A_23_P161852 1821 AGI_HUM1_OLIGO_A_23_P124078 4205 AGI_HUM1_OLIGO_A_23_P155335 8635 AGI_HUM1_OLIGO_A_23_P29983 12524 AGI_HUM1_OLIGO_A_23_P82088 1584 AGI_HUM1_OLIGO_A_23_P121030 3053 AGI_HUM1_OLIGO_A_23_P140487 4089 AGI_HUM1_OLIGO_A_23_P153937 10260 AGI_HUM1_OLIGO_A_23_P51499 10292 AGI_HUM1_OLIGO_A_23_P5189 1058 AGI_HUM1_OLIGO_A_23_P114075 8996 AGI_HUM1_OLIGO_A_23_P34943 1051 AGI_HUM1_OLIGO_A_23_P113972 9297 AGI_HUM1_OLIGO_A_23_P38795 13459 AGI_HUM1_OLIGO_A_23_P95085 1450 AGI_HUM1_OLIGO_A_23_P119472 1693 AGI_HUM1_OLIGO_A_23_P122485 772 AGI_HUM1_OLIGO_A_23_P110105 2579 AGI_HUM1_OLIGO_A_23_P134014 1138 AGI_HUM1_OLIGO_A_23_P115246 6283 AGI_HUM1_OLIGO_A_23_P207680 3689 AGI_HUM1_OLIGO_A_23_P148858 8580 AGI_HUM1_OLIGO_A_23_P29296 13121 AGI_HUM1_OLIGO_A_23_P90419 8705 AGI_HUM1_OLIGO_A_23_P30972 11941 AGI_HUM1_OLIGO_A_23_P74241 3008 AGI_HUM1_OLIGO_A_23_P139872 3153 AGI_HUM1_OLIGO_A_23_P141759 9009 AGI_HUM1_OLIGO_A_23_P35055 2007 AGI_HUM1_OLIGO_A_23_P126844 13274 AGI_HUM1_OLIGO_A_23_P92476 6183 AGI_HUM1_OLIGO_A_23_P206501 12851 AGI_HUM1_OLIGO_A_23_P86889 13718 AGI_HUM1_OLIGO_A_23_P98659 9374 AGI_HUM1_OLIGO_A_23_P39766 5336 AGI_HUM1_OLIGO_A_23_P17083 8310 AGI_HUM1_OLIGO_A_23_P259901 4230 AGI_HUM1_OLIGO_A_23_P155735 6229 AGI_HUM1_OLIGO_A_23_P207036 12059 AGI_HUM1_OLIGO_A_23_P75903 4014 AGI_HUM1_OLIGO_A_23_P152991 8258 AGI_HUM1_OLIGO_A_23_P259189 11111 AGI_HUM1_OLIGO_A_23_P63032
Recommended publications
  • Final Copy 2018 09 25 Gaunt

    Final Copy 2018 09 25 Gaunt

    This electronic thesis or dissertation has been downloaded from Explore Bristol Research, http://research-information.bristol.ac.uk Author: Gaunt, Jess Title: A Viral Approach to Translatome Profiling of CA1 Neurons During Associative Recognition Memory Formation General rights Access to the thesis is subject to the Creative Commons Attribution - NonCommercial-No Derivatives 4.0 International Public License. A copy of this may be found at https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode This license sets out your rights and the restrictions that apply to your access to the thesis so it is important you read this before proceeding. Take down policy Some pages of this thesis may have been removed for copyright restrictions prior to having it been deposited in Explore Bristol Research. However, if you have discovered material within the thesis that you consider to be unlawful e.g. breaches of copyright (either yours or that of a third party) or any other law, including but not limited to those relating to patent, trademark, confidentiality, data protection, obscenity, defamation, libel, then please contact [email protected] and include the following information in your message: •Your contact details •Bibliographic details for the item, including a URL •An outline nature of the complaint Your claim will be investigated and, where appropriate, the item in question will be removed from public view as soon as possible. A Viral Approach to Translatome Profiling of CA1 Neurons During Associative Recognition Memory Formation Jessica Ruth Gaunt A dissertation submitted to the University of Bristol in accordance with the requirements for award of the degree of Doctor of Philosophy in the Faculty of Health Sciences, Bristol Medical School.
  • Emerging Roles of ARHGAP33 in Intracellular Trafficking of Trkb And

    Emerging Roles of ARHGAP33 in Intracellular Trafficking of Trkb And

    ARTICLE Received 21 Oct 2015 | Accepted 4 Jan 2016 | Published 3 Feb 2016 DOI: 10.1038/ncomms10594 OPEN Emerging roles of ARHGAP33 in intracellular trafficking of TrkB and pathophysiology of neuropsychiatric disorders Takanobu Nakazawa1,2,3, Ryota Hashimoto4,5, Kazuto Sakoori1, Yuki Sugaya1, Asami Tanimura1, Yuki Hashimotodani1, Kazutaka Ohi4, Hidenaga Yamamori4,6, Yuka Yasuda4, Satomi Umeda-Yano6, Yuji Kiyama7, Kohtarou Konno8, Takeshi Inoue2, Kazumasa Yokoyama2, Takafumi Inoue9, Shusuke Numata10, Tohru Ohnuma11, Nakao Iwata12, Norio Ozaki13, Hitoshi Hashimoto3,5,14, Masahiko Watanabe8, Toshiya Manabe7, Tadashi Yamamoto2,15, Masatoshi Takeda4,5 & Masanobu Kano1 Intracellular trafficking of receptor proteins is essential for neurons to detect various extra- cellular factors during the formation and refinement of neural circuits. However, the precise mechanisms underlying the trafficking of neurotrophin receptors to synapses remain elusive. Here, we demonstrate that a brain-enriched sorting nexin, ARHGAP33, is a new type of regulator for the intracellular trafficking of TrkB, a high-affinity receptor for brain-derived neurotrophic factor. ARHGAP33 knockout (KO) mice exhibit reduced expression of synaptic TrkB, impaired spine development and neuropsychiatric disorder-related behavioural abnormalities. These deficits are rescued by specific pharmacological enhancement of TrkB signalling in ARHGAP33 KO mice. Mechanistically, ARHGAP33 interacts with SORT1 to cooperatively regulate TrkB trafficking. Human ARHGAP33 is associated with brain pheno- types and reduced SORT1 expression is found in patients with schizophrenia. We propose that ARHGAP33/SORT1-mediated TrkB trafficking is essential for synapse development and that the dysfunction of this mechanism may be a new molecular pathology of neuropsychiatric disorders. 1 Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
  • The Interactome of KRAB Zinc Finger Proteins Reveals the Evolutionary History of Their Functional Diversification

    The Interactome of KRAB Zinc Finger Proteins Reveals the Evolutionary History of Their Functional Diversification

    Resource The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification Pierre-Yves Helleboid1,†, Moritz Heusel2,†, Julien Duc1, Cécile Piot1, Christian W Thorball1, Andrea Coluccio1, Julien Pontis1, Michaël Imbeault1, Priscilla Turelli1, Ruedi Aebersold2,3,* & Didier Trono1,** Abstract years ago (MYA) (Imbeault et al, 2017). Their products harbor an N-terminal KRAB (Kru¨ppel-associated box) domain related to that of Krüppel-associated box (KRAB)-containing zinc finger proteins Meisetz (a.k.a. PRDM9), a protein that originated prior to the diver- (KZFPs) are encoded in the hundreds by the genomes of higher gence of chordates and echinoderms, and a C-terminal array of zinc vertebrates, and many act with the heterochromatin-inducing fingers (ZNF) with sequence-specific DNA-binding potential (Urru- KAP1 as repressors of transposable elements (TEs) during early tia, 2003; Birtle & Ponting, 2006; Imbeault et al, 2017). KZFP genes embryogenesis. Yet, their widespread expression in adult tissues multiplied by gene and segment duplication to count today more and enrichment at other genetic loci indicate additional roles. than 350 and 700 representatives in the human and mouse Here, we characterized the protein interactome of 101 of the ~350 genomes, respectively (Urrutia, 2003; Kauzlaric et al, 2017). A human KZFPs. Consistent with their targeting of TEs, most KZFPs majority of human KZFPs including all primate-restricted family conserved up to placental mammals essentially recruit KAP1 and members target sequences derived from TEs, that is, DNA trans- associated effectors. In contrast, a subset of more ancient KZFPs posons, ERVs (endogenous retroviruses), LINEs, SINEs (long and rather interacts with factors related to functions such as genome short interspersed nuclear elements, respectively), or SVAs (SINE- architecture or RNA processing.
  • Noelia Díaz Blanco

    Noelia Díaz Blanco

    Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr.
  • The Landscape of Human Mutually Exclusive Splicing

    The Landscape of Human Mutually Exclusive Splicing

    bioRxiv preprint doi: https://doi.org/10.1101/133215; this version posted May 2, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. The landscape of human mutually exclusive splicing Klas Hatje1,2,#,*, Ramon O. Vidal2,*, Raza-Ur Rahman2, Dominic Simm1,3, Björn Hammesfahr1,$, Orr Shomroni2, Stefan Bonn2§ & Martin Kollmar1§ 1 Group of Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany 2 Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany 3 Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science, Georg-August-University Göttingen, Germany § Corresponding authors # Current address: Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland $ Current address: Research and Development - Data Management (RD-DM), KWS SAAT SE, Einbeck, Germany * These authors contributed equally E-mail addresses: KH: [email protected], RV: [email protected], RR: [email protected], DS: [email protected], BH: [email protected], OS: [email protected], SB: [email protected], MK: [email protected] - 1 - bioRxiv preprint doi: https://doi.org/10.1101/133215; this version posted May 2, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
  • Supp Table 6.Pdf

    Supp Table 6.Pdf

    Supplementary Table 6. Processes associated to the 2037 SCL candidate target genes ID Symbol Entrez Gene Name Process NM_178114 AMIGO2 adhesion molecule with Ig-like domain 2 adhesion NM_033474 ARVCF armadillo repeat gene deletes in velocardiofacial syndrome adhesion NM_027060 BTBD9 BTB (POZ) domain containing 9 adhesion NM_001039149 CD226 CD226 molecule adhesion NM_010581 CD47 CD47 molecule adhesion NM_023370 CDH23 cadherin-like 23 adhesion NM_207298 CERCAM cerebral endothelial cell adhesion molecule adhesion NM_021719 CLDN15 claudin 15 adhesion NM_009902 CLDN3 claudin 3 adhesion NM_008779 CNTN3 contactin 3 (plasmacytoma associated) adhesion NM_015734 COL5A1 collagen, type V, alpha 1 adhesion NM_007803 CTTN cortactin adhesion NM_009142 CX3CL1 chemokine (C-X3-C motif) ligand 1 adhesion NM_031174 DSCAM Down syndrome cell adhesion molecule adhesion NM_145158 EMILIN2 elastin microfibril interfacer 2 adhesion NM_001081286 FAT1 FAT tumor suppressor homolog 1 (Drosophila) adhesion NM_001080814 FAT3 FAT tumor suppressor homolog 3 (Drosophila) adhesion NM_153795 FERMT3 fermitin family homolog 3 (Drosophila) adhesion NM_010494 ICAM2 intercellular adhesion molecule 2 adhesion NM_023892 ICAM4 (includes EG:3386) intercellular adhesion molecule 4 (Landsteiner-Wiener blood group)adhesion NM_001001979 MEGF10 multiple EGF-like-domains 10 adhesion NM_172522 MEGF11 multiple EGF-like-domains 11 adhesion NM_010739 MUC13 mucin 13, cell surface associated adhesion NM_013610 NINJ1 ninjurin 1 adhesion NM_016718 NINJ2 ninjurin 2 adhesion NM_172932 NLGN3 neuroligin
  • Structure and Expression Analyses of SVA Elements in Relation to Functional Genes

    Structure and Expression Analyses of SVA Elements in Relation to Functional Genes

    pISSN 1598-866X eISSN 2234-0742 Genomics Inform 2013;11(3):142-148 G&I Genomics & Informatics http://dx.doi.org/10.5808/GI.2013.11.3.142 ORIGINAL ARTICLE Structure and Expression Analyses of SVA Elements in Relation to Functional Genes Yun-Jeong Kwon, Yuri Choi, Jungwoo Eo, Yu-Na Noh, Jeong-An Gim, Yi-Deun Jung, Ja-Rang Lee, Heui-Soo Kim* Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Korea SINE-VNTR-Alu (SVA) elements are present in hominoid primates and are divided into 6 subfamilies (SVA-A to SVA-F) and active in the human population. Using a bioinformatic tool, 22 SVA element-associated genes are identified in the human genome. In an analysis of genomic structure, SVA elements are detected in the 5′ untranslated region (UTR) of HGSNAT (SVA-B), MRGPRX3 (SVA-D), HYAL1 (SVA-F), TCHH (SVA-F), and ATXN2L (SVA-F) genes, while some elements are observed in the 3′UTR of SPICE1 (SVA-B), TDRKH (SVA-C), GOSR1 (SVA-D), BBS5 (SVA-D), NEK5 (SVA-D), ABHD2 (SVA-F), C1QTNF7 (SVA-F), ORC6L (SVA-F), TMEM69 (SVA-F), and CCDC137 (SVA-F) genes. They could contribute to exon extension or supplying poly A signals. LEPR (SVA-C), ALOX5 (SVA-D), PDS5B (SVA-D), and ABCA10 (SVA-F) genes also showed alternative transcripts by SVA exonization events. Dominant expression of HYAL1_SVA appeared in lung tissues, while HYAL1_noSVA showed ubiquitous expression in various human tissues. Expression of both transcripts (TDRKH_SVA and TDRKH_noSVA) of the TDRKH gene appeared to be ubiquitous.
  • WO 2012/174282 A2 20 December 2012 (20.12.2012) P O P C T

    WO 2012/174282 A2 20 December 2012 (20.12.2012) P O P C T

    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2012/174282 A2 20 December 2012 (20.12.2012) P O P C T (51) International Patent Classification: David [US/US]; 13539 N . 95th Way, Scottsdale, AZ C12Q 1/68 (2006.01) 85260 (US). (21) International Application Number: (74) Agent: AKHAVAN, Ramin; Caris Science, Inc., 6655 N . PCT/US20 12/0425 19 Macarthur Blvd., Irving, TX 75039 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 14 June 2012 (14.06.2012) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, English (25) Filing Language: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, Publication Language: English DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, (30) Priority Data: KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, 61/497,895 16 June 201 1 (16.06.201 1) US MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 61/499,138 20 June 201 1 (20.06.201 1) US OM, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SC, SD, 61/501,680 27 June 201 1 (27.06.201 1) u s SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, 61/506,019 8 July 201 1(08.07.201 1) u s TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
  • Genome-Wide Association Study Identifies 44 Independent Genomic Loci for Self-Reported Adult Hearing Difficulty in the UK Biobank Cohort

    Genome-Wide Association Study Identifies 44 Independent Genomic Loci for Self-Reported Adult Hearing Difficulty in the UK Biobank Cohort

    bioRxiv preprint doi: https://doi.org/10.1101/549071; this version posted February 14, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Genome-wide association study identifies 44 independent genomic loci for self-reported adult hearing difficulty in the UK Biobank cohort Helena RR. Wells1,2, Maxim B. Freidin1, Fatin N. Zainul Abidin2, Antony Payton3, Piers Dawes4, Kevin J. Munro4,5, Cynthia C. Morton4,5,6, David R. Moore4,7, #*Sally J Dawson2, #*Frances MK. Williams1 1Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London 2UCL Ear Institute, University College London 3Division of Informatics, Imaging & Data Sciences, The University of Manchester 4Manchester Centre for Audiology and Deafness, The University of Manchester 5Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre 6Departments of Obstetrics and Gynecology and of Pathology, Brigham and Women’s Hospital, Harvard Medical School 7Cincinnati Children's Hospital Medical Centre, Department of Otolaryngology, University of Cincinnati College of Medicine #Joint senior authors *Corresponding authors 1 bioRxiv preprint doi: https://doi.org/10.1101/549071; this version posted February 14, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Age-related hearing impairment (ARHI) is the most common sensory impairment in the aging population; a third of individuals are affected by disabling hearing loss by the age of 651.
  • HHS Public Access Author Manuscript

    HHS Public Access Author Manuscript

    HHS Public Access Author manuscript Author Manuscript Author ManuscriptJAMA Psychiatry Author Manuscript. Author Author Manuscript manuscript; available in PMC 2015 August 03. Published in final edited form as: JAMA Psychiatry. 2014 June ; 71(6): 657–664. doi:10.1001/jamapsychiatry.2014.176. Identification of Pathways for Bipolar Disorder A Meta-analysis John I. Nurnberger Jr, MD, PhD, Daniel L. Koller, PhD, Jeesun Jung, PhD, Howard J. Edenberg, PhD, Tatiana Foroud, PhD, Ilaria Guella, PhD, Marquis P. Vawter, PhD, and John R. Kelsoe, MD for the Psychiatric Genomics Consortium Bipolar Group Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Nurnberger, Koller, Edenberg, Foroud); Institute of Psychiatric Research, Department of Psychiatry, Indiana University School of Medicine, Indianapolis (Nurnberger, Foroud); Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism Intramural Research Program, Bethesda, Maryland (Jung); Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis (Edenberg); Functional Genomics Laboratory, Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine (Guella, Vawter); Department of Psychiatry, School of Medicine, Corresponding Author: John I. Nurnberger Jr, MD, PhD, Institute of Psychiatric Research, Department of Psychiatry, Indiana University School of Medicine, 791 Union Dr, Indianapolis, IN 46202 ([email protected]). Author Contributions: Drs Koller and Vawter had full access to all of the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis. Study concept and design: Nurnberger, Koller, Edenberg, Vawter. Acquisition, analysis, or interpretation of data: All authors. Drafting of the manuscript: Nurnberger, Koller, Jung, Vawter.
  • Nº Ref Uniprot Proteína Péptidos Identificados Por MS/MS 1 P01024

    Nº Ref Uniprot Proteína Péptidos Identificados Por MS/MS 1 P01024

    Document downloaded from http://www.elsevier.es, day 26/09/2021. This copy is for personal use. Any transmission of this document by any media or format is strictly prohibited. Nº Ref Uniprot Proteína Péptidos identificados 1 P01024 CO3_HUMAN Complement C3 OS=Homo sapiens GN=C3 PE=1 SV=2 por 162MS/MS 2 P02751 FINC_HUMAN Fibronectin OS=Homo sapiens GN=FN1 PE=1 SV=4 131 3 P01023 A2MG_HUMAN Alpha-2-macroglobulin OS=Homo sapiens GN=A2M PE=1 SV=3 128 4 P0C0L4 CO4A_HUMAN Complement C4-A OS=Homo sapiens GN=C4A PE=1 SV=1 95 5 P04275 VWF_HUMAN von Willebrand factor OS=Homo sapiens GN=VWF PE=1 SV=4 81 6 P02675 FIBB_HUMAN Fibrinogen beta chain OS=Homo sapiens GN=FGB PE=1 SV=2 78 7 P01031 CO5_HUMAN Complement C5 OS=Homo sapiens GN=C5 PE=1 SV=4 66 8 P02768 ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2 66 9 P00450 CERU_HUMAN Ceruloplasmin OS=Homo sapiens GN=CP PE=1 SV=1 64 10 P02671 FIBA_HUMAN Fibrinogen alpha chain OS=Homo sapiens GN=FGA PE=1 SV=2 58 11 P08603 CFAH_HUMAN Complement factor H OS=Homo sapiens GN=CFH PE=1 SV=4 56 12 P02787 TRFE_HUMAN Serotransferrin OS=Homo sapiens GN=TF PE=1 SV=3 54 13 P00747 PLMN_HUMAN Plasminogen OS=Homo sapiens GN=PLG PE=1 SV=2 48 14 P02679 FIBG_HUMAN Fibrinogen gamma chain OS=Homo sapiens GN=FGG PE=1 SV=3 47 15 P01871 IGHM_HUMAN Ig mu chain C region OS=Homo sapiens GN=IGHM PE=1 SV=3 41 16 P04003 C4BPA_HUMAN C4b-binding protein alpha chain OS=Homo sapiens GN=C4BPA PE=1 SV=2 37 17 Q9Y6R7 FCGBP_HUMAN IgGFc-binding protein OS=Homo sapiens GN=FCGBP PE=1 SV=3 30 18 O43866 CD5L_HUMAN CD5 antigen-like OS=Homo
  • Spatial and Temporal Aspects of Signalling 6 1

    Spatial and Temporal Aspects of Signalling 6 1

    r r r Cell Signalling Biology Michael J. Berridge Module 6 Spatial and Temporal Aspects of Signalling 6 1 Module 6 Spatial and Temporal Aspects of Signalling Synopsis The function and efficiency of cell signalling pathways are very dependent on their organization both in space and time. With regard to spatial organization, signalling components are highly organized with respect to their cellular location and how they transmit information from one region of the cell to another. This spatial organization of signalling pathways depends on the molecular interactions that occur between signalling components that use signal transduction domains to construct signalling pathways. Very often, the components responsible for information transfer mechanisms are held in place by being attached to scaffolding proteins to form macromolecular signalling complexes. Sometimes these macromolecular complexes can be organized further by being localized to specific regions of the cell, as found in lipid rafts and caveolae or in the T-tubule regions of skeletal and cardiac cells. Another feature of the spatial aspects concerns the local Another important temporal aspect is timing and signal and global aspects of signalling. The spatial organization of integration, which relates to the way in which functional signalling molecules mentioned above can lead to highly interactions between signalling pathways are determined localized signalling events, but when the signalling mo- by both the order and the timing of their presentations. lecules are more evenly distributed, signals can spread The organization of signalling systems in both time and more globally throughout the cell. In addition, signals space greatly enhances both their efficiency and versatility.