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Association of Gene Ontology Categories with Decay Rate for Hepg2 Experiments These Tables Show Details for All Gene Ontology Categories

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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) FASTER 4.83E-04 16.1 (0.7) 5.1 (0.1) OVER 0 GO:0000074 regulation of cell cycle 575 0.178 (0.014) 0.133 (0.002) FASTER 6.18E-04 7.7 (0.5) 5.0 (0.1) OVER 2.29E-07 GO:0007178 transmembrane receptor protein serine/threonine kinase signaling48 pathway0.316 (0.057) 0.134 (0.002) FASTER 6.58E-04 21.8 (3.8) 5.1 (0.1) OVER 4.44E-06 GO:0007179 TGFbeta receptor signaling pathway 44 0.301 (0.055) 0.134 (0.002) FASTER 1.19E-03 19.7 (3.8) 5.1 (0.1) OVER 7.31E-05 GO:0042127 regulation of cell proliferation 295 0.190 (0.020) 0.133 (0.002) FASTER 2.23E-03 12.2 (0.9) 5.0 (0.1) OVER 2.26E-15 GO:0006596 polyamine biosynthesis 36 0.239 (0.038) 0.134 (0.002) FASTER 3.07E-03 27.2 (1.9) 5.1 (0.1) OVER 0 GO:0008285 negative regulation of cell proliferation 167 0.215 (0.031) 0.133 (0.002) FASTER 3.73E-03 14.1 (1.2) 5.1 (0.1) OVER 3.06E-15 GO:0000079 regulation of CDK activity 100 0.225 (0.035) 0.134 (0.002) FASTER 4.81E-03 11.5 (1.4) 5.1 (0.1) OVER 3.01E-06 GO:0006367 transcription initiation from Pol II promoter 78 0.254 (0.046) 0.133 (0.002) FASTER 4.89E-03 14.1 (2.8) 5.1 (0.1) OVER 5.36E-04 GO:0006915 apoptosis 428 0.175 (0.017) 0.133 (0.002) FASTER 6.35E-03 7.1 (0.6) 5.1 (0.1) OVER 2.30E-04 GO:0012501 programmed cell death 428 0.175 (0.017) 0.133 (0.002) FASTER 6.35E-03 7.1 (0.6) 5.1 (0.1) OVER 2.30E-04 GO:0006352 transcription initiation 86 0.241 (0.043) 0.134 (0.002) FASTER 6.65E-03 12.8 (2.5) 5.1 (0.1) OVER 0.001 GO:0000086 G2/M transition of mitotic cell cycle 112 0.214 (0.032) 0.134 (0.002) FASTER 6.75E-03 11.9 (1.3) 5.1 (0.1) OVER 9.23E-08 GO:0006512 ubiquitin cycle 184 0.183 (0.020) 0.134 (0.002) FASTER 6.98E-03 7.4 (1.2) 5.1 (0.1) NO SIG 0.025 GO:0007275 development 1082 0.156 (0.009) 0.133 (0.002) FASTER 9.16E-03 6.7 (0.3) 5.0 (0.1) OVER 8.01E-07 GO:0007049 cell cycle 1204 0.155 (0.009) 0.133 (0.002) NO SIG 0.011 6.7 (0.4) 5.0 (0.1) OVER 8.41E-06 GO:0006595 polyamine metabolism 40 0.215 (0.035) 0.134 (0.002) NO SIG 0.011 24.5 (1.7) 5.1 (0.1) OVER 0 GO:0019748 secondary metabolism 40 0.215 (0.035) 0.134 (0.002) NO SIG 0.011 24.5 (1.7) 5.1 (0.1) OVER 0 GO:0009653 morphogenesis 613 0.161 (0.012) 0.133 (0.002) NO SIG 0.012 7.4 (0.4) 5.1 (0.1) OVER 1.49E-07 GO:0009887 organogenesis 613 0.161 (0.012) 0.133 (0.002) NO SIG 0.012 7.4 (0.4) 5.1 (0.1) OVER 1.49E-07 GO:0007397 histogenesis and organogenesis 101 0.220 (0.038) 0.134 (0.002) NO SIG 0.012 14.8 (1.3) 5.1 (0.1) OVER 6.88E-14 GO:0008219 cell death 448 0.169 (0.016) 0.133 (0.002) NO SIG 0.013 6.7 (0.5) 5.1 (0.1) OVER 0.001 GO:0042401 biogenic amine biosynthesis 56 0.213 (0.036) 0.134 (0.002) NO SIG 0.013 20.3 (1.6) 5.1 (0.1) OVER 0 GO:0006468 protein amino acid phosphorylation 729 0.160 (0.012) 0.133 (0.002) NO SIG 0.014 6.0 (0.5) 5.1 (0.1) NO SIG 0.028 GO:0016265 death 455 0.167 (0.016) 0.133 (0.002) NO SIG 0.017 6.6 (0.5) 5.1 (0.1) OVER 0.002 GO:0016071 mRNA metabolism 43 0.228 (0.045) 0.134 (0.002) NO SIG 0.019 5.8 (2.7) 5.1 (0.1) NO SIG 0.409 GO:0008099 synaptic vesicle endocytosis 37 0.237 (0.052) 0.134 (0.002) NO SIG 0.023 18.2 (2.8) 5.1 (0.1) OVER 2.00E-06 GO:0042398 amino acid derivative biosynthesis 60 0.201 (0.034) 0.134 (0.002) NO SIG 0.023 18.9 (1.5) 5.1 (0.1) OVER 0 GO:0006298 mismatch repair 37 0.242 (0.055) 0.134 (0.002) NO SIG 0.024 11.2 (3.4) 5.1 (0.1) NO SIG 0.036 GO:0045005 maintenance of fidelity during DNA dependent DNA replication37 0.242 (0.055) 0.134 (0.002) NO SIG 0.024 11.2 (3.4) 5.1 (0.1) NO SIG 0.036 GO:0000278 mitotic cell cycle 719 0.156 (0.012) 0.133 (0.002) NO SIG 0.029 6.6 (0.5) 5.1 (0.1) OVER 0.002 GO:0000122 negative regulation of transcription from Pol II promoter 100 0.201 (0.036) 0.134 (0.002) NO SIG 0.032 15.0 (1.5) 5.1 (0.1) OVER 1.73E-11 GO:0016481 negative regulation of transcription 100 0.201 (0.036) 0.134 (0.002) NO SIG 0.032 15.0 (1.5) 5.1 (0.1) OVER 1.73E-11 GO:0016310 phosphorylation 765 0.155 (0.012) 0.133 (0.002) NO SIG 0.033 5.8 (0.5) 5.1 (0.1) NO SIG 0.083 GO:0000082 G1/S transition of mitotic cell cycle 165 0.182 (0.026) 0.134 (0.002) NO SIG 0.034 7.9 (1.0) 5.1 (0.1) OVER 0.004 GO:0006511 ubiquitin-dependent protein degradation 320 0.159 (0.014) 0.134 (0.002) NO SIG 0.039 6.1 (0.8) 5.1 (0.1) NO SIG 0.104 GO:0000087 M phase of mitotic cell cycle 257 0.167 (0.019) 0.134 (0.002) NO SIG 0.041 7.8 (0.9) 5.1 (0.1) OVER 8.30E-04 GO:0007067 mitosis 253 0.166 (0.019) 0.134 (0.002) NO SIG 0.047 8.0 (0.9) 5.1 (0.1) OVER 6.04E-04 GO:0006796 phosphate metabolism 1021 0.150 (0.010) 0.133 (0.002) NO SIG 0.050 5.4 (0.4) 5.1 (0.1) NO SIG 0.207 GO:0007369 gastrulation 27 0.244 (0.070) 0.134 (0.002) NO SIG 0.057 10.9 (4.8) 5.1 (0.1) NO SIG 0.113 GO:0009790 embryonic development 27 0.244 (0.070) 0.134 (0.002) NO SIG 0.057 10.9 (4.8) 5.1 (0.1) NO SIG 0.113 GO:0009792 embryonic development (sensu Animalia) 27 0.244 (0.070) 0.134 (0.002) NO SIG 0.057 10.9 (4.8) 5.1 (0.1) NO SIG 0.113 GO:0019941 protein-ligand dependent protein degradation 328 0.156 (0.014) 0.134 (0.002) NO SIG 0.058 6.0 (0.8) 5.1 (0.1) NO SIG 0.137 GO:0006360 transcription from Pol I promoter 48 0.193 (0.038) 0.134 (0.002) NO SIG 0.060 10.1 (2.0) 5.1 (0.1) OVER 0.006 GO:0007093 mitotic checkpoint 32 0.204 (0.046) 0.134 (0.002) NO SIG 0.065 4.3 (2.7) 5.1 (0.1) NO SIG 0.383 GO:0000280 nuclear division 304 0.162 (0.018) 0.134 (0.002) NO SIG 0.065 7.2 (0.8) 5.1 (0.1) OVER 0.004 GO:0007020 microtubule nucleation 50 0.209 (0.050) 0.134 (0.002) NO SIG 0.067 7.8 (1.6) 5.1 (0.1) NO SIG 0.048 GO:0000279 M phase 320 0.160 (0.018) 0.134 (0.002) NO SIG 0.072 6.8 (0.7) 5.1 (0.1) NO SIG 0.011 GO:0000075 cell cycle checkpoint 71 0.191 (0.039) 0.134 (0.002) NO SIG 0.072 5.7 (2.1) 5.1 (0.1) NO SIG 0.390 GO:0007276 gametogenesis 140 0.173 (0.028) 0.134 (0.002) NO SIG 0.082 8.6 (0.9) 5.1 (0.1) OVER 9.62E-05 GO:0009888 histogenesis 86 0.184 (0.037) 0.134 (0.002) NO SIG 0.086 7.2 (1.7) 5.1 (0.1) NO SIG 0.109 GO:0007021 tubulin folding 32 0.224 (0.067) 0.134 (0.002) NO SIG 0.088 10.2 (1.6) 5.1 (0.1) OVER 7.76E-04 GO:0007323 pheromone processing 43 0.195 (0.046) 0.134 (0.002) NO SIG 0.092 8.4 (1.5) 5.1 (0.1) NO SIG 0.015 GO:0016485 protein processing 43 0.195 (0.046) 0.134 (0.002) NO SIG 0.092 8.4 (1.5) 5.1 (0.1) NO SIG 0.015 GO:0006879 iron homeostasis 40 0.199 (0.049) 0.134 (0.002) NO SIG 0.093 12.5 (0.0) 5.1 (0.1) OVER 0 GO:0006383 transcription from Pol III promoter 42 0.211 (0.061) 0.134 (0.002) NO SIG 0.104 4.8 (2.3) 5.1 (0.1) NO SIG 0.436 GO:0006974 response to DNA damage 83 0.197 (0.052) 0.134 (0.002) NO SIG 0.111 9.9 (1.4) 5.1 (0.1) OVER 4.96E-04 GO:0007167 enzyme linked receptor protein signaling pathway 173 0.161 (0.023) 0.134 (0.002) NO SIG 0.113 7.6 (1.2) 5.1 (0.1) NO SIG 0.021 GO:0009611 response to wounding 147 0.169 (0.029) 0.134 (0.002) NO SIG 0.114 8.8 (1.2) 5.1 (0.1) OVER 0.001 GO:0008625 induction of apoptosis via death domain receptors 35 0.206 (0.060) 0.134 (0.002) NO SIG 0.116 6.4 (2.1) 5.1 (0.1) NO SIG 0.283 GO:0007089 start control point of mitotic cell cycle 32 0.216 (0.069) 0.134 (0.002) NO SIG 0.117 6.2 (3.4) 5.1 (0.1) NO SIG 0.374 GO:0001501 skeletal development 122 0.167 (0.029) 0.134 (0.002) NO SIG 0.124 10.6 (1.0) 5.1 (0.1) OVER 5.89E-08 GO:0000003 reproduction 165 0.162 (0.025) 0.134 (0.002) NO SIG 0.125 7.4 (0.8) 5.1 (0.1) OVER 0.003 GO:0007324 a-factor processing (proteolytic) 35 0.197 (0.055) 0.134 (0.002) NO SIG 0.127 10.3 (1.9) 5.1 (0.1) OVER 0.003 GO:0009292 genetic exchange 55 0.178 (0.040) 0.134 (0.002) NO SIG 0.130 6.6 (1.2) 5.1 (0.1) NO SIG 0.111 GO:0007283 spermatogenesis 94 0.175 (0.037) 0.134 (0.002) NO SIG 0.131 10.5 (1.0) 5.1 (0.1) OVER 2.23E-08 GO:0008371 obsolete 436 0.152 (0.017) 0.134 (0.002) NO SIG 0.135 6.4 (0.6) 5.1 (0.1) NO SIG 0.019 GO:0006464 protein modification 1436 0.143 (0.008) 0.133 (0.002) NO SIG 0.135 4.7 (0.3) 5.2 (0.1) NO SIG 0.086 GO:0006261 DNA dependent DNA replication 171 0.161 (0.025) 0.134 (0.002) NO SIG 0.141 5.0 (1.1) 5.1 (0.1) NO SIG 0.437 GO:0006576 biogenic amine metabolism 75 0.165 (0.029) 0.134 (0.002) NO SIG 0.141 15.2 (1.2) 5.1 (0.1) OVER 4.43E-18 GO:0008284 positive regulation of cell proliferation
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    CHARACTERIZATION OF NUDIX HYDROLASES: A UTILITARIAN SUPERFAMILY OF ENZYMES By Andres Hernandez de la Peña A dissertation submitted to the Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland August, 2015 Abstract The present work details the structural and enzymatic characterization of Nudix hydrolases from three different organisms – Bdellovibrio bacteriovorus, Mycobacterium tuberculosis, and Tetrahymena thermophila. Each of these Nudix enzymes presents unique questions about their physiological function within their organism which are answered with a combination of structural biology, genetic manipulation, enzyme kinetics, and a wide range of protein assays. We demonstrate that RenU, from M. tuberculosis, is part of Redox Homeostasis Control System (RHOCS), which senses and regulates NADH concentrations. This control systems involves two other proteins, the serine/threonine protein kinase G (pknG) and the L13 ribosomal subunits, without which the bacterium fails to evade lysosomal delivery and falls prey to the oxidative arsenal of the macrophage host. Bd-NDPSase, a Nudix enzyme encoded by the B. bacteriovorus gene BD3179, localizes to the periplasmic space of the bacterium and hydrolyses at least four nucleoside diphosphate sugars in vitro. Through atomic-resolution models from X-ray diffraction, we identified a motif that differentiates this hydrolase from the similar, but more substrate specific, ADP- ribose hydrolase from E. coli. Lastly, we show that Nud1p from T. thermophila is a member of the Ezl1p complex, the histone methyltransferase Polycomb Group homologue of this protozoan. With the use of in vitro enzymatic assays we show, in addition, that Nu1dp hydrolyses CoA preferentially over acetyl-CoA and other nucleoside derivatives.
  • Experimental Validation of the Regulated Expression of Large Numbers of Non-Coding Rnas from the Mouse Genome

    Experimental Validation of the Regulated Expression of Large Numbers of Non-Coding Rnas from the Mouse Genome

    Downloaded from genome.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Article Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome Timothy Ravasi,1,4,5 Harukazu Suzuki,2,4 Ken C. Pang,1,3,4 Shintaro Katayama,2,4 Masaaki Furuno,2,4,6 Rie Okunishi,2 Shiro Fukuda,2 Kelin Ru,1 Martin C. Frith,1,2 M. Milena Gongora,1 Sean M. Grimmond,1 David A. Hume,1 Yoshihide Hayashizaki,2 and John S. Mattick1,7 1ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia; 2Laboratory for Genome Exploration Research Group, RIKEN Genomic Science Center, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; 3T Cell Laboratory, Ludwig Institute for Cancer Research, Austin & Repatriation Medical Centre, Heidelberg VIC 3084, Australia Recent large-scale analyses of mainly full-length cDNA libraries generated from a variety of mouse tissues indicated that almost half of all representative cloned sequences did not contain an apparent protein-coding sequence, and were putatively derived from non-protein-coding RNA (ncRNA) genes. However, many of these clones were singletons and the majority were unspliced, raising the possibility that they may be derived from genomic DNA or unprocessed pre-mRNA contamination during library construction, or alternatively represent nonspecific “transcriptional noise.” Here we show, using reverse transcriptase-dependent PCR, microarray, and Northern blot analyses, that many of these clones were derived from genuine transcripts of unknown function whose expression appears to be regulated.
  • RNF2 Antibody Order 021-34695924 Orders@Ab-Mart.Com Support 400-6123-828 50Ul Support1@Ab-Mart.Com 100 Ul √ √ Web

    RNF2 Antibody Order 021-34695924 [email protected] Support 400-6123-828 50Ul [email protected] 100 Ul √ √ Web

    TD7403 RNF2 Antibody Order 021-34695924 [email protected] Support 400-6123-828 50ul [email protected] 100 uL √ √ Web www.ab-mart.com.cn Description: E3 ubiquitin-protein ligase that mediates monoubiquitination of 'Lys-119' of histone H2A (H2AK119Ub), thereby playing a central role in histone code and gene regulation. H2AK119Ub gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. May be involved in the initiation of both imprinted and random X inactivation (By similarity). Essential component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility. E3 ubiquitin-protein ligase activity is enhanced by BMI1/PCGF4. Acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity (Probable). Association with the chromosomal DNA is cell-cycle dependent. In resting B- and T-lymphocytes, interaction with AURKB leads to block its activity, thereby maintaining transcription in resting lymphocytes (By similarity). Uniprot:Q99496 Alternative Names： BAP 1; BAP1; DING; DinG protein; E3 ubiquitin protein ligase RING 2; E3 ubiquitin protein ligase RING2; E3 ubiquitin-protein ligase RING2; HIP2 interacting protein 3; HIP2- interacting protein 3; HIPI 3; HIPI3; Huntingtin interacting protein 2 interacting protein 3; Huntingtin-interacting protein 2-interacting protein 3; OTTHUMP00000060668; Polycomb M33 interacting protein Ring 1B; Polycomb M33 interacting protein Ring1B; Protein DinG; RING 1B; RING 2; RING finger protein 1B; RING finger protein 2; RING finger protein BAP 1; RING finger protein BAP-1; RING finger protein BAP1; RING1b; RING2_HUMAN; RNF 2; Rnf2; Specificity: RNF2 Antibody detects endogenous levels of total RNF2.
  • Product Data Sheet

    Product Data Sheet

    For research purposes only, not for human use Product Data Sheet RNF2 siRNA (Human) Catalog # Source Reactivity Applications CRH4092 Synthetic H RNAi Description siRNA to inhibit RNF2 expression using RNA interference Specificity RNF2 siRNA (Human) is a target-specific 19-23 nt siRNA oligo duplexes designed to knock down gene expression. Form Lyophilized powder Gene Symbol RNF2 Alternative Names BAP1; DING; HIPI3; RING1B; E3 ubiquitin-protein ligase RING2; Huntingtin-interacting protein 2-interacting protein 3; HIP2-interacting protein 3; Protein DinG; RING finger protein 1B; RING1b; RING finger protein 2; RING finger protein BAP-1 Entrez Gene 6045 (Human) SwissProt Q99496 (Human) Purity > 97% Quality Control Oligonucleotide synthesis is monitored base by base through trityl analysis to ensure appropriate coupling efficiency. The oligo is subsequently purified by affinity-solid phase extraction. The annealed RNA duplex is further analyzed by mass spectrometry to verify the exact composition of the duplex. Each lot is compared to the previous lot by mass spectrometry to ensure maximum lot-to-lot consistency. Components We offers pre-designed sets of 3 different target-specific siRNA oligo duplexes of human RNF2 gene. Each vial contains 5 nmol of lyophilized siRNA. The duplexes can be transfected individually or pooled together to achieve knockdown of the target gene, which is most commonly assessed by qPCR or western blot. Our siRNA oligos Application key: E- ELISA, WB- Western blot, IH- Immunohistochemistry, IF- Immunofluorescence, FC-
  • 'Next- Generation' Sequencing Data Analysis

    'Next- Generation' Sequencing Data Analysis

    Novel Algorithm Development for ‘Next- Generation’ Sequencing Data Analysis Agne Antanaviciute Submitted in accordance with the requirements for the degree of Doctor of Philosophy University of Leeds School of Medicine Leeds Institute of Biomedical and Clinical Sciences 12/2017 ii The candidate confirms that the work submitted is her own, except where work which has formed part of jointly-authored publications has been included. The contribution of the candidate and the other authors to this work has been explicitly given within the thesis where reference has been made to the work of others. This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement ©2017 The University of Leeds and Agne Antanaviciute The right of Agne Antanaviciute to be identified as Author of this work has been asserted by her in accordance with the Copyright, Designs and Patents Act 1988. Acknowledgements I would like to thank all the people who have contributed to this work. First and foremost, my supervisors Dr Ian Carr, Professor David Bonthron and Dr Christopher Watson, who have provided guidance, support and motivation. I could not have asked for a better supervisory team. I would also like to thank my collaborators Dr Belinda Baquero and Professor Adrian Whitehouse for opening new, interesting research avenues. A special thanks to Dr Belinda Baquero for all the hard wet lab work without which at least half of this thesis would not exist. Thanks to everyone at the NGS Facility – Carolina Lascelles, Catherine Daley, Sally Harrison, Ummey Hany and Laura Crinnion – for the generation of NGS data used in this work and creating a supportive and stimulating work environment.