CATEGORY a TERM COUNT b P VALUE GENE FAMILIES: REPRESENTATIVE GENE SYMBOLS c. Annotation Cluster 1 Enrichment Score: 1.
|
|
|
- Jonah Lee
- 5 years ago
- Views:
Transcription
1 Table S7 GO term and functional classification enrichment analysis using DAVID for gene families that are expanded in the Drosophila suzukii genome as compared to 14 Drosophila species analyzed in this study. CATEGORY a TERM COUNT b P VALUE GENE FAMILIES: REPRESENTATIVE GENE SYMBOLS c Annotation Cluster 1 Enrichment Score: GO: glycerol metabolic E-03 Gpdh, CG18135, Gyk GO: alditol metabolic E-03 Gpdh, CG18135, Gyk GO: polyol metabolic E-02 Gpdh, CG18135, Gyk Annotation Cluster 2 Enrichment Score: GO: regulation of cellular protein metabolic GO: negative regulation of macromolecule metabolic GO: negative regulation of cellular protein metabolic GO: negative regulation of protein metabolic E-03 Acp76A, PEK, Adam, mrpl11, Tollo, Spn77Bc, Su(var)205, nos, elav E-03 WRNexo, Acp76A, mrpl11, Spn77Bc, Su(var)205, elav, mael, Hsc70-4, PEK, E(spl)m8-HLH, fkh, lolal, nos E-02 Acp76A, PEK, Spn77Bc, nos, elav E-02 Acp76A, PEK, Spn77Bc, nos, elav SWISSPROT PIR translation regulation E-02 PEK, mrpl11, nos a Categories used in DAVID analysis include GO sub-ontologies for Biological Process (BP), Molecular Function (MF), and CC (Cellular Component), as well as keywords from SwissProt PIR (Protein Information Resource) and protein domains from the Interpro database. b Count represents the number of gene families c Gene symbol for representative, most highly annotated member of each gene family is shown. All annotations shown here are from D. melanogaster. 38 SI J. C. Chiu et al.
2 GO: regulation of translation E-02 PEK, Adam, mrpl11, nos, elav GO: posttranscriptional regulation of gene expression E-02 Hsc70-4, PEK, Adam, mrpl11, nos, elav Annotation Cluster 3 Enrichment Score: SWISSPROT PIR Chaperone E-02 CG7394, CG11267, Cnx99A, Tcp-1zeta GO: protein folding E-02 Hsc70-4, CG11267, Cnx99A, Tcp-1zeta, FKBP59 GOTERM MF GO: unfolded protein binding E-02 Hsc70-4, CG11267, Cnx99A, Tcp-1zeta Annotation Cluster 4 Enrichment Score: GO: detection of stimulus E-02 Or49a, Calx, CheB42a, Galphaq, FKBP59 SWISSPROT PIR sensory transduction E-02 Or49a, Or69a, Galphaq, FKBP59, Or22a GO: detection of light stimulus E-02 Calx, Galphaq, FKBP59 GO: detection of abiotic stimulus E-02 Calx, Galphaq, FKBP59 GO: detection of external stimulus E-02 Calx, Galphaq, FKBP59 Annotation Cluster 5 Enrichment Score: INTERPRO IPR007087:Zinc finger, C2H2-type E-02 CG6689, term, CG1647, CG16779, CG10669, Meics, CG5316, CG4360, CG3065, CG11966, CG4318 INTERPRO IPR015880:Zinc finger, C2H2-like E-02 CG6689, CG1647, CG16779, CG10669, Meics, CG5316, CG4360, CG3065, CG11966, noi, CG4318 J. C. Chiu et al. 39 SI
3 INTERPRO IPR012934:Zinc finger, AD-type E-02 CG6689, CG1647, CG10669, Meics, CG4318 INTERPRO IPR013087:Zinc finger, C2H2-type/integrase, DNA-binding E-02 CG11966, CG6689, CG16779, CG10669, Meics, CG4360, CG3065 SMART SM00355:ZnF_C2H E-02 CG6689, CG1647, CG16779, CG10669, Meics, CG5316, CG4360, CG3065, CG11966, noi, CG4318 Annotation Cluster 6 Enrichment Score: SWISSPROT PIR sensory transduction E-02 Or49a, Or69a, Galphaq, FKBP59, Or22a GOTERM MF GO: odorant binding E-02 Obp83ef, Or49a, Obp51a, CheB42a, Or69a, Or22a GO: G-protein coupled receptor protein signaling pathway E-02 Or49a, Tk, D2R, Or69a, Galphaq, Gr85a, mth, Pk1r, Or22a SWISSPROT PIR transducer E-02 Or49a, D2R, Or69a, Galphaq, Gr85a, mth, Pk1r, Or22a GO: sensory perception E-02 Obp83ef, Or49a, Obp51a, Or69a, Galphaq, Gr85a, FKBP59, Or22a SWISSPROT PIR g-protein coupled receptor E-02 Or49a, D2R, Or69a, Gr85a, mth, Pk1r, Or22a INTERPRO IPR004117:Olfactory receptor, Drosophila E-02 Or49a, Or69a, Or22a GO: plasma membrane E-02 D2R, Tollo, Or69a, Gr85a, Rac1, Cnx99A, Cad74A, Oscp, Pk1r, Mical, Syn1, Or49a, Calx, Galphaq, mth, FKBP59, Or22a PIR_SUPERFAMILY PIRSF008678:odorant receptor E-02 Or49a, Or69a, Or22a GO: neurological system E-02 Obp83ef, scramb1, Obp51a, cher, Or69a, Gr85a, Rac1, Hsc70-4, Or49a, Galphaq, mth, FKBP59, Or22a 40 SI J. C. Chiu et al.
4 Annotation Cluster 7 Enrichment Score: SWISSPROT PIR mitochondrion inner membrane E-02 CG7394, ATPsyn-d, ATPsyn-b, Oscp, CG9603 GO: mitochondrial protontransporting ATP synthase complex E-02 ATPsyn-d, ATPsyn-b, Oscp SWISSPROT PIR Hydrogen ion transport E-02 ATPsyn-d, ATPsyn-b, Oscp GO: nucleotide biosynthetic GO: ribonucleotide biosynthetic GO: ribonucleotide metabolic GO: proton-transporting ATP synthase complex GO: nucleobase, nucleoside and nucleotide biosynthetic GO: nucleobase, nucleoside, nucleotide and nucleic acid biosynthetic GO: nitrogen compound biosynthetic E-02 ATPsyn-d, pug, CG6767, Ada, ATPsyn-b, Oscp E-02 ATPsyn-d, CG6767, Ada, ATPsyn-b, Oscp E-02 ATPsyn-d, CG6767, Ada, ATPsyn-b, Oscp E-02 ATPsyn-d, ATPsyn-b, Oscp E-02 ATPsyn-d, pug, CG6767, Ada, ATPsyn-b, Oscp E-02 ATPsyn-d, pug, CG6767, Ada, ATPsyn-b, Oscp E-02 ATPsyn-d, CG11899, pug, CG6767, Ada, ATPsyn-b, Odc1, Oscp J. C. Chiu et al. 41 SI
5 GO: purine nucleotide biosynthetic E-02 ATPsyn-d, pug, Ada, ATPsyn-b, Oscp GO: mitochondrial membrane part E-02 CG7394, ATPsyn-d, CG4769, ATPsyn-b, Oscp, CG9603 GO: purine nucleotide metabolic E-02 ATPsyn-d, pug, Ada, ATPsyn-b, Oscp GO: mitochondrial part E-02 CG7394, ATPsyn-d, mrpl11, CG4769, ATPsyn-b, Hmt-1, Dic1, CG11267, CG9547, mrpl20, Oscp, CG9603 GO: mitochondrial inner membrane E-02 CG7394, ATPsyn-d, CG4769, ATPsyn-b, Hmt-1, Oscp, CG9603 Annotation Cluster 8 Enrichment Score: GOTERM MF GOTERM MF GO: serine-type endopeptidase inhibitor activity GO: endopeptidase inhibitor activity E-02 Acp76A, CG31515, Spn77Bc, CG E-02 Acp76A, CG31515, Spn77Bc, CG3604 GOTERM MF GO: peptidase inhibitor activity E-02 Acp76A, CG31515, Spn77Bc, CG SI J. C. Chiu et al.
Biological Process Term Enrichment
Biological Process Term Enrichment cellular protein localization cellular macromolecule localization intracellular protein transport intracellular transport generation of precursor metabolites and energy
GO ID GO term Number of members GO: translation 225 GO: nucleosome 50 GO: calcium ion binding 76 GO: structural
GO ID GO term Number of members GO:0006412 translation 225 GO:0000786 nucleosome 50 GO:0005509 calcium ion binding 76 GO:0003735 structural constituent of ribosome 170 GO:0019861 flagellum 23 GO:0005840
Comparative RNA-seq analysis of transcriptome dynamics during petal development in Rosa chinensis
Title Comparative RNA-seq analysis of transcriptome dynamics during petal development in Rosa chinensis Author list Yu Han 1, Huihua Wan 1, Tangren Cheng 1, Jia Wang 1, Weiru Yang 1, Huitang Pan 1* & Qixiang
1 GO: regulation of cell size E-04 2 GO: negative regulation of cell growth GO:
Table S2: The biological modulated by mir-5701 Sr. No Term Id 1 Term Name 2 Hit Gene Number 3 P-Value 4 1 GO:0008361 regulation of cell size 9 4.37E-04 2 GO:0030308 negative regulation of cell growth 8
Gene Ontology and Functional Enrichment. Genome 559: Introduction to Statistical and Computational Genomics Elhanan Borenstein
Gene Ontology and Functional Enrichment Genome 559: Introduction to Statistical and Computational Genomics Elhanan Borenstein The parsimony principle: A quick review Find the tree that requires the fewest
S1 Gene ontology (GO) analysis of the network alignment results
1 Supplementary Material for Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model Hyundoo Jeong 1, Xiaoning Qian 1 and
BMD645. Integration of Omics
BMD645 Integration of Omics Shu-Jen Chen, Chang Gung University Dec. 11, 2009 1 Traditional Biology vs. Systems Biology Traditional biology : Single genes or proteins Systems biology: Simultaneously study
Genome Annotation. Bioinformatics and Computational Biology. Genome sequencing Assembly. Gene prediction. Protein targeting.
Genome Annotation Bioinformatics and Computational Biology Genome Annotation Frank Oliver Glöckner 1 Genome Analysis Roadmap Genome sequencing Assembly Gene prediction Protein targeting trna prediction
GENE ONTOLOGY (GO) Wilver Martínez Martínez Giovanny Silva Rincón
GENE ONTOLOGY (GO) Wilver Martínez Martínez Giovanny Silva Rincón What is GO? The Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products in
Large-scale GO analysis reveals gene expression level and variation are functional and location related
Large-scale GO analysis reveals gene expression level and variation are functional and location related Simon M. Lin 1, Pan Du 1, and Warren A. Kibbe 1 1 Robert H. Lurie Comprehensive Cancer Center, Northwestern
Supplementary Information 16
Supplementary Information 16 Cellular Component % of Genes 50 45 40 35 30 25 20 15 10 5 0 human mouse extracellular other membranes plasma membrane cytosol cytoskeleton mitochondrion ER/Golgi translational
JMJ14-HA. Col. Col. jmj14-1. jmj14-1 JMJ14ΔFYR-HA. Methylene Blue. Methylene Blue
Fig. S1 JMJ14 JMJ14 JMJ14ΔFYR Methylene Blue Col jmj14-1 JMJ14-HA Methylene Blue Col jmj14-1 JMJ14ΔFYR-HA Fig. S1. The expression level of JMJ14 and truncated JMJ14 with FYR (FYRN + FYRC) domain deletion
Lecture 3: A basic statistical concept
Lecture 3: A basic statistical concept P value In statistical hypothesis testing, the p value is the probability of obtaining a result at least as extreme as the one that was actually observed, assuming
Mean Hes score. Threshold
Mean Hes score 0.1 0.09 Common 0.08 Family 0.07 0.06 0.05 0.04 0.03 0.02 0.01 0 0 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 Threshold SUPPLEMENTARY FIG. 1. Trend of mean Hes scores calculated based on the
the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together Chemical structure Covalent bond Ionic bond
Chemical structure the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together Covalent bond bond formed by the sharing of valence electrons between atoms Ionic bond
Genome Annotation Project Presentation
Halogeometricum borinquense Genome Annotation Project Presentation Loci Hbor_05620 & Hbor_05470 Presented by: Mohammad Reza Najaf Tomaraei Hbor_05620 Basic Information DNA Coordinates: 527,512 528,261
Chapter 12: Intracellular sorting
Chapter 12: Intracellular sorting Principles of intracellular sorting Principles of intracellular sorting Cells have many distinct compartments (What are they? What do they do?) Specific mechanisms are
Bio 101 General Biology 1
Revised: Fall 2016 Bio 101 General Biology 1 COURSE OUTLINE Prerequisites: Prerequisite: Successful completion of MTE 1, 2, 3, 4, and 5, and a placement recommendation for ENG 111, co-enrollment in ENF
The biomolecules of terrestrial life
Functional groups in biomolecules Groups of atoms that are responsible for the chemical properties of biomolecules The biomolecules of terrestrial life Planets and Astrobiology (2017-2018) G. Vladilo 1
A Protein Ontology from Large-scale Textmining?
A Protein Ontology from Large-scale Textmining? Protege-Workshop Manchester, 07-07-2003 Kai Kumpf, Juliane Fluck and Martin Hofmann Instructive mistakes: a narrative Aim: Protein ontology that supports
Gene Ontology and overrepresentation analysis
Gene Ontology and overrepresentation analysis Kjell Petersen J Express Microarray analysis course Oslo December 2009 Presentation adapted from Endre Anderssen and Vidar Beisvåg NMC Trondheim Overview How
De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes
Additional_file Ashrafi_et_al_0_Pepper_Annotation_Supp_0070.docx A Microsoft-Word 007 file with figures comparing the results of BlastGO for GeneChip (Sanger-EST) and transcriptome assemlies of pepper
BIOCHEMISTRY NOTES - UNIT 2-
BIOCHEMISTRY NOTES - UNIT 2- ATOMS - the basic unit of matter. Contains subatomic particles o (+ charge) o (no charge/neutral) o (- charge) Protons and neutrons have about the same mass. Electrons are
Outline. Terminologies and Ontologies. Communication and Computation. Communication. Outline. Terminologies and Vocabularies.
Page 1 Outline 1. Why do we need terminologies and ontologies? Terminologies and Ontologies Iwei Yeh yeh@smi.stanford.edu 04/16/2002 2. Controlled Terminologies Enzyme Classification Gene Ontology 3. Ontologies
Introduction to Bioinformatics
CSCI8980: Applied Machine Learning in Computational Biology Introduction to Bioinformatics Rui Kuang Department of Computer Science and Engineering University of Minnesota kuang@cs.umn.edu History of Bioinformatics
Chapter 6- An Introduction to Metabolism*
Chapter 6- An Introduction to Metabolism* *Lecture notes are to be used as a study guide only and do not represent the comprehensive information you will need to know for the exams. The Energy of Life
REVIEW 1: BIOCHEMISTRY UNIT. A. Top 10 If you learned anything from this unit, you should have learned:
Period Date REVIEW 1: BIOCHEMISTRY UNIT A. Top 10 If you learned anything from this unit, you should have learned: 1. All living matter made up of CHONPS 2. Bonds a. covalent bonds are strong b. hydrogen
Scale in the biological world
Scale in the biological world 2 A cell seen by TEM 3 4 From living cells to atoms 5 Compartmentalisation in the cell: internal membranes and the cytosol 6 The Origin of mitochondria: The endosymbion hypothesis
Supplementary Table 3. Membrane/Signaling/Neural Genes of the DmSP. FBgn CG5265 acetyltransferase amino acid metabolism
Supplementary Table 3 Membrane/Signaling/Neural Genes of the DmSP FlyBase ID Gene Name Molecular function summary Membrane Biological process summary FBgn0038486 CG5265 acetyltransferase amino acid metabolism
Virginia Western Community College BIO 101 General Biology I
BIO 101 General Biology I Prerequisites Successful completion of MTE 1, 2, 3, 4, and 5; and a placement recommendation for ENG 111, co-enrollment in ENF 3/ENG 111, or successful completion of all developmental
Motif Gene Ontology Anatomy Ontology
83.4 465 small molecule metabolic process (2.2e-34) hydrolase activity (3.5e-28) biosynthetic process (5.7e-25) locomotion (8.1e-22) anatomical structure development (3.0e-21) locomotion (8.8e-59) anatomical
Chapter 002 The Chemistry of Biology
Chapter 002 The Chemistry of Biology Multiple Choice Questions 1. Anything that occupies space and has mass is called A. Atomic B. Living C. Matter D. Energy E. Space 2. The electrons of an atom are A.
2. In regards to the fluid mosaic model, which of the following is TRUE?
General Biology: Exam I Sample Questions 1. How many electrons are required to fill the valence shell of a neutral atom with an atomic number of 24? a. 0 the atom is inert b. 1 c. 2 d. 4 e. 6 2. In regards
Comparative Features of Multicellular Eukaryotic Genomes
Comparative Features of Multicellular Eukaryotic Genomes C elegans A thaliana O. Sativa D. melanogaster M. musculus H. sapiens Size (Mb) 97 115 389 120 2500 2900 # Genes 18,425 25,498 37,544 13,601 30,000
Review of Lecture 1. Be able to identify the cell components for bacterial, animal, and plant cells and know their functions Properties of water
Review of Lecture 1 Be able to identify the cell components for bacterial, animal, and plant cells and know their functions Properties of water Bulk properties Atomic properties Weak acids and bases Acid
Supplemental Material
Supplemental Material Protocol S1 The PromPredict algorithm considers the average free energy over a 100nt window and compares it with the the average free energy over a downstream 100nt window separated
I. Molecules & Cells. A. Unit One: The Nature of Science. B. Unit Two: The Chemistry of Life. C. Unit Three: The Biology of the Cell.
I. Molecules & Cells A. Unit One: The Nature of Science a. How is the scientific method used to solve problems? b. What is the importance of controls? c. How does Darwin s theory of evolution illustrate
Runs of homozygosity and evidence of adaptation in Nellore cattle. Elisa Peripolli UNESP/FCAV - Brazil
Runs of homozygosity and evidence of adaptation in Nellore cattle Elisa Peripolli UNESP/FCAV - Brazil Objective 1. Identify autozygosity islands based on ROH in the genome of the Nellore cattle. 2. Examine
I. Molecules and Cells: Cells are the structural and functional units of life; cellular processes are based on physical and chemical changes.
I. Molecules and Cells: Cells are the structural and functional units of life; cellular processes are based on physical and chemical changes. A. Chemistry of Life B. Cells 1. Water How do the unique chemical
Integration of functional genomics data
Integration of functional genomics data Laboratoire Bordelais de Recherche en Informatique (UMR) Centre de Bioinformatique de Bordeaux (Plateforme) Rennes Oct. 2006 1 Observations and motivations Genomics
Transcriptome analysis of leaf tissue from Bermudagrass (Cynodon dactylon) using a normalised cdna library
Ó CSIRO 2008 ISSN 1445-4408 10.1071/FP08133_AC Functional Plant Biology, 2008, 35, 585 594 Transcriptome analysis of leaf tissue from Bermudagrass (Cynodon dactylon) using a normalised cdna library Changsoo
2.1 Atoms, Ions, and Molecules
2.1 Atoms, Ions, and Molecules Living things consist of atoms of different elements. An atom is the smallest basic unit of matter. An element is one type of atom. 6 elements make up 99% of all living things
Networks & pathways. Hedi Peterson MTAT Bioinformatics
Networks & pathways Hedi Peterson (peterson@quretec.com) MTAT.03.239 Bioinformatics 03.11.2010 Networks are graphs Nodes Edges Edges Directed, undirected, weighted Nodes Genes Proteins Metabolites Enzymes
Lecture 7 Cell Biolog y ٢٢٢ ١
Lecture 7 ١ Mitochondria ٢ Mitochondria Mitochondria are the energy factories of the cells. The energy currency for the work that animals must do is the energy-rich molecule adenosine triphosphate (ATP).
Biology Unit 2 Chemistry of Life (Ch. 6) Guided Notes
Name Biology Unit 2 Chemistry of Life (Ch. 6) Guided Notes Atoms, Elements, and Chemical Bonding I can draw atom models and identify the # protons, # neutrons, and # electrons in an atom. I can identify
2. All of the following are accurate statements regarding the above graph EXCEPT:
General Biology 115 Summer 2014: Exam I Form A Name: 1. Which of the following best explains why FADH2 yields less ATP than NADH during cell respiration? a. Energy captured by FADH2 contributes less to
Chapter 2. Introduction: Chapter Chemical Basis of Life. Structure of Matter:
Chapter 2.1-2.2 Read text 2.1 and describe why chemistry is important in understanding life. Read text 2.2 and discuss how atomic structure determines how atoms interact. Also describe the types of chemical
Dr. Nafith Abu Tarboush
8 Dr. Nafith Abu Tarboush June 30 th 2013 Ahmad Ayyat Nucleic Acids: Molecules that carries information for growth and production of cells, and they are Polymers of "Nucleotides" (the monomers).01 Nucleotide
Prerequisites Properties of allosteric enzymes. Basic mechanisms involving regulation of metabolic pathways.
Case 16 Allosteric Regulation of ATCase Focus concept An enzyme involved in nucleotide synthesis is subject to regulation by a variety of combinations of nucleotides. Prerequisites Properties of allosteric
EVPP 110 Lecture Exam #1 Study Questions Fall 2003 Dr. Largen
EVPP 110 Lecture Exam #1 Study Questions Fall 2003 Dr. Largen These study questions are meant to focus your study of the material for the first exam. The absence here of a topic or point covered in lecture
Unit 1: Chemistry - Guided Notes
Scientific Method Notes: Unit 1: Chemistry - Guided Notes 1 Common Elements in Biology: Atoms are made up of: 1. 2. 3. In order to be stable, an atom of an element needs a full valence shell of electrons.
MOLECULAR CELL BIOLOGY
1 Lodish Berk Kaiser Krieger scott Bretscher Ploegh Matsudaira MOLECULAR CELL BIOLOGY SEVENTH EDITION CHAPTER 13 Moving Proteins into Membranes and Organelles Copyright 2013 by W. H. Freeman and Company
2.1 The Nature of Matter
2.1 The Nature of Matter Lesson Objectives Identify the three subatomic particles found in atoms. Explain how all of the isotopes of an element are similar and how they are different. Explain how compounds
AP Bio-Ms.Bell Unit#3 Cellular Energies Name
AP Bio-Ms.Bell Unit#3 Cellular Energies Name 1. Base your answer to the following question on the image below. 7. Base your answer to the following question on Which of the following choices correctly
AP BIOLOGY BIOCHEMISTRY MULTIPLE CHOICE EXAM (RAVEN CHAPTERS 2, 3)
Period Date AP BIOLOGY BIOCHEMISTRY MULTIPLE CHOICE EXAM (RAVEN CHAPTERS 2, 3) 1. Which of the following is an example of a hydrogen bond? (90:09) A. The peptide bond between amino acids in a protein B.
Introduction. Gene expression is the combined process of :
1 To know and explain: Regulation of Bacterial Gene Expression Constitutive ( house keeping) vs. Controllable genes OPERON structure and its role in gene regulation Regulation of Eukaryotic Gene Expression
Biomolecules. Energetics in biology. Biomolecules inside the cell
Biomolecules Energetics in biology Biomolecules inside the cell Energetics in biology The production of energy, its storage, and its use are central to the economy of the cell. Energy may be defined as
Amino Acid Structures from Klug & Cummings. 10/7/2003 CAP/CGS 5991: Lecture 7 1
Amino Acid Structures from Klug & Cummings 10/7/2003 CAP/CGS 5991: Lecture 7 1 Amino Acid Structures from Klug & Cummings 10/7/2003 CAP/CGS 5991: Lecture 7 2 Amino Acid Structures from Klug & Cummings
2: CHEMICAL COMPOSITION OF THE BODY
1 2: CHEMICAL COMPOSITION OF THE BODY CHAPTER OVERVIEW This chapter provides an overview of basic chemical principles that are important to understanding human physiological function and ultimately homeostasis.
A Brief Overview of Biochemistry. And I mean BRIEF!
A Brief Overview of Biochemistry And I mean BRIEF! Introduction A. Chemistry deals with the composition of substances and how they change. B. A knowledge of chemistry is necessary for the understanding
2) Matter composed of a single type of atom is known as a(n) 2) A) element. B) mineral. C) electron. D) compound. E) molecule.
MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question. 1) Which of the following is a particle found in the nucleus of an atom and that has no electrical
Chapter 15 Active Reading Guide Regulation of Gene Expression
Name: AP Biology Mr. Croft Chapter 15 Active Reading Guide Regulation of Gene Expression The overview for Chapter 15 introduces the idea that while all cells of an organism have all genes in the genome,
ENV SCI 22 GROUP QUIZ WEEK 2
ENV SCI 22 GROUP QUIZ WEEK 2 ph OF ACIDS AND BASES 1) A decrease of one unit in the ph scale above represents a tenfold increase in the hydrogen ion concentration of a solution. For example, a solution
Unit Two Chemistry of the Human Body
I. Introduction to atoms Unit Two Chemistry of the Human Body A. Chemistry is the branch of science that concerns itself with the structure of matter, including the interaction between atoms. 1. Atoms-
Nature of matter. Chemical bond is a force that joins atoms
Nature of matter Atom the smallest unit of matter that cannot be broken down by chemical means The subatomic particles of an atom consist of protons, neutrons and electrons Element is a pure substance
Analysis and visualization of protein-protein interactions. Olga Vitek Assistant Professor Statistics and Computer Science
1 Analysis and visualization of protein-protein interactions Olga Vitek Assistant Professor Statistics and Computer Science 2 Outline 1. Protein-protein interactions 2. Using graph structures to study
Energy Converion: Mitochondria and Chloroplasts. Pınar Tulay, Ph.D.
Energy Converion: Mitochondria and Chloroplasts Pınar Tulay, Ph.D. pintulay@gmail.com Energy Conversion Prokaryotes use plasma membrane to produce adenosine triphosphate (ATP) used in the cell function
Protein function studies: history, current status and future trends
19 3 2007 6 Chinese Bulletin of Life Sciences Vol. 19, No. 3 Jun., 2007 1004-0374(2007)03-0294-07 ( 100871) Q51A Protein function studies: history, current status and future trends MA Jing, GE Xi, CHANG
-max_target_seqs: maximum number of targets to report
Review of exercise 1 tblastn -num_threads 2 -db contig -query DH10B.fasta -out blastout.xls -evalue 1e-10 -outfmt "6 qseqid sseqid qstart qend sstart send length nident pident evalue" Other options: -max_target_seqs:
AP BIOLOGY SUMMER ASSIGNMENT
AP BIOLOGY SUMMER ASSIGNMENT Welcome to EDHS Advanced Placement Biology! The attached summer assignment is required for all AP Biology students for the 2011-2012 school year. The assignment consists of
Written Exam 15 December Course name: Introduction to Systems Biology Course no
Technical University of Denmark Written Exam 15 December 2008 Course name: Introduction to Systems Biology Course no. 27041 Aids allowed: Open book exam Provide your answers and calculations on separate
Lesson Overview. 8.3 The Process of Photosynthesis
8.3 The Process of Photosynthesis The Light-Dependent Reactions: Generating ATP and NADPH The light-dependent reactions encompass the steps of photosynthesis that directly involve sunlight. The light-dependent
GACE Biology Assessment Test I (026) Curriculum Crosswalk
Subarea I. Cell Biology: Cell Structure and Function (50%) Objective 1: Understands the basic biochemistry and metabolism of living organisms A. Understands the chemical structures and properties of biologically
Topology. 1 Introduction. 2 Chromosomes Topology & Counts. 3 Genome size. 4 Replichores and gene orientation. 5 Chirochores.
Topology 1 Introduction 2 3 Genome size 4 Replichores and gene orientation 5 Chirochores 6 G+C content 7 Codon usage 27 marc.bailly-bechet@univ-lyon1.fr The big picture Eukaryota Bacteria Many linear chromosomes
What Organelle Makes Proteins According To The Instructions Given By Dna
What Organelle Makes Proteins According To The Instructions Given By Dna This is because it contains the information needed to make proteins. assemble enzymes and other proteins according to the directions
Systematic approaches to study cancer cell metabolism
Systematic approaches to study cancer cell metabolism Kivanc Birsoy Laboratory of Metabolic Regulation and Genetics The Rockefeller University, NY Cellular metabolism is complex ~3,000 metabolic genes
Improving Gene Functional Analysis in Ethylene-induced Leaf Abscission using GO and ProteInOn
Improving Gene Functional Analysis in Ethylene-induced Leaf Abscission using GO and ProteInOn Sara Domingos 1, Cátia Pesquita 2, Francisco M. Couto 2, Luis F. Goulao 3, Cristina Oliveira 1 1 Instituto
Biology Chapter 2: The Chemistry of Life. title 4 pictures, with color (black and white don t count!)
33 Biology Chapter 2: The Chemistry of Life title 4 pictures, with color (black and white don t count!) 34 Chapter 2: The Chemistry of Life Goals Highlight all unknown words 35-36 Chapter 2: The Chemistry
The body has three primary lines of defense against changes in hydrogen ion concentration in the body fluids.
ph and Nucleic acids Hydrogen Ion (H+) concentration is precisely regulated. The H+ concentration in the extracellular fluid is maintained at a very low level, averaging 0.00000004Eq/L. normal variations
A genome sequence based discriminator for vancomycin intermediate Staphyolococcus aureus Supplementary Methods
1 Journal of Bacteriology Computational Biology Section 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 Supplementary Information for: A genome sequence based discriminator
Cell Organelles. a review of structure and function
Cell Organelles a review of structure and function TEKS and Student Expectations (SE s) B.4 Science concepts. The student knows that cells are the basic structures of all living things with specialized
Plant Stimuli pp Topic 3: Plant Behaviour Ch. 39. Plant Behavioural Responses. Plant Hormones. Plant Hormones pp
Topic 3: Plant Behaviour Ch. 39 Plants exist in environments that are constantly changing. Like animals, plants must be able to detect and react to stimuli in the environment. Unlike animals, plants can
Advanced Higher Biology. Unit 1- Cells and Proteins 2c) Membrane Proteins
Advanced Higher Biology Unit 1- Cells and Proteins 2c) Membrane Proteins Membrane Structure Phospholipid bilayer Transmembrane protein Integral protein Movement of Molecules Across Membranes Phospholipid
Activation of a receptor. Assembly of the complex
Activation of a receptor ligand inactive, monomeric active, dimeric When activated by growth factor binding, the growth factor receptor tyrosine kinase phosphorylates the neighboring receptor. Assembly
Chapter 1. Topic: Overview of basic principles
Chapter 1 Topic: Overview of basic principles Four major themes of biochemistry I. What are living organism made from? II. How do organism acquire and use energy? III. How does an organism maintain its
Comparison of Human Protein-Protein Interaction Maps
Comparison of Human Protein-Protein Interaction Maps Matthias E. Futschik 1, Gautam Chaurasia 1,2, Erich Wanker 2 and Hanspeter Herzel 1 1 Institute for Theoretical Biology, Charité, Humboldt-Universität
Foundations in Microbiology Seventh Edition
Lecture PowerPoint to accompany Foundations in Microbiology Seventh Edition Talaro Chapter 2 The Chemistry of Biology Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Missouri Educator Gateway Assessments
Missouri Educator Gateway Assessments June 2014 Content Domain Range of Competencies Approximate Percentage of Test Score I. Science and Engineering Practices 0001 0003 21% II. Biochemistry and Cell Biology
(A) Glucose (B) Amino acids (C) Fatty acids (D) Nucleotides (E) Monosaccharides
High School Biology - Problem Drill 02: The Chemical Basis of Life Question No. 1 of 10 1. Proteins are composed of which of these monomers? Question #01 (A) Glucose (B) Amino acids (C) Fatty acids (D)
Living and nonliving matter is composed of atoms.
Chemistry Topics Covered Atomic structure and interactions Properties of Water Biological Molecules: carbohydrates, lipids, nucleic acids, and proteins Central Dogma: DNA à RNA à Protein Protein Structure:
Translation Part 2 of Protein Synthesis
Translation Part 2 of Protein Synthesis IN: How is transcription like making a jello mold? (be specific) What process does this diagram represent? A. Mutation B. Replication C.Transcription D.Translation
CHEMISTRY. 2 Types of Properties Associated with Matter. Composition of Matter. Physical: properties that do not change the identity of the substance
CHEMISTRY Composition of Matter Matter Mass Anything that occupies space and has mass Quantity of matter an object has Weight Pull of gravity on an object 2 Types of Properties Associated with Matter Physical:
Supplementary Figure 1 The number of differentially expressed genes for uniparental males (green), uniparental females (yellow), biparental males
Supplementary Figure 1 The number of differentially expressed genes for males (green), females (yellow), males (red), and females (blue) in caring vs. control comparisons in the caring gene set and the
Microbiology with Diseases by Taxonomy, 5e (Bauman) Chapter 2 The Chemistry of Microbiology. 2.1 Multiple Choice Questions
Microbiology with Diseases by Taxonomy, 5e (Bauman) Chapter 2 The Chemistry of Microbiology 2.1 Multiple Choice Questions 1) Which of the following does not contribute significantly to the mass of an atom?
Cellular Neuroanatomy I The Prototypical Neuron: Soma. Reading: BCP Chapter 2
Cellular Neuroanatomy I The Prototypical Neuron: Soma Reading: BCP Chapter 2 Functional Unit of the Nervous System The functional unit of the nervous system is the neuron. Neurons are cells specialized
Computational Chemical Biology Research Group. Connecting Compound Structures to Biological Effects by Gene-Expression Profiling
Computational Chemical Biology Research Group Connecting Compound Structures to Biological Effects by Gene-Expression Profiling David Jaramillo Mentor: Mathias Wawer PI: Paul Clemons Summer Research Program
Prediction of protein function from sequence analysis
Prediction of protein function from sequence analysis Rita Casadio BIOCOMPUTING GROUP University of Bologna, Italy The omic era Genome Sequencing Projects: Archaea: 74 species In Progress:52 Bacteria:
Life Depends on Photosynthesis
Photosynthesis Life Depends on Photosynthesis Most energy Comes from the Sun Life Depends on Photosynthesis Most energy Comes from the Sun Life Depends on Photosynthesis Most energy Comes from the Sun
CSCE555 Bioinformatics. Protein Function Annotation
CSCE555 Bioinformatics Protein Function Annotation Why we need to do function annotation? Fig from: Network-based prediction of protein function. Molecular Systems Biology 3:88. 2007 What s function? The
Big Idea 1: The process of evolution drives the diversity and unity of life. Sunday, August 28, 16
Big Idea 1: The process of evolution drives the diversity and unity of life. Enduring understanding 1.B: Organisms are linked by lines of descent from common ancestry. Essential knowledge 1.B.1: Organisms