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Pensamientos sobre FDR Alberto Medina 10 th, Dec. 2012
FDR. ¿Protein or Peptide?
How we define an experiment?
False positives ¿FDR por Fracción o Experimento?
12 exp. Grouping by experiment
12 exp. Grouping by cell line (3)
Chr16 proteins. NO FDR 388pr/319.
1 exp = 10 searches FDR 1% protein. 292/239 (genes).
1 exp = 1 search (10 exps). FDR 1% protein. 316/260
1 exp = 1 search (10 exps). FDR 1% protein. 316/260
1 exp = 1 search (10 exps). FDR 1% peptide. 336/279
Multiplication Find the missing value x __ = 32.
Quest Review Unit 2. Get same bases; set exponents = 1. 2 x = x = 2 7 x = 7 2. 3 x = /2x = 3 5 1/2x = 5 x = x = x = 2 5 x.
De Novo Sequencing v.s. Database Search Bin Ma School of Computer Science University of Waterloo Ontario, Canada.
Cells of E. coli bacteria Allow cells to respond to changes in their environment Only make proteins when they are needed.
File 5 MOUSE sequences used in target gene promoter regions to detect NFATc1 protein binding by ChIP.
Questions # 1 DNA carries the code for making proteins.
ProteoRed WG1-WG2 Meeting Pamplona, December 10th 2013 PME10 PROPOSALS.
Genome Browsing with the UCSC Genome Browser
Methanol/Chloroform precipitation In-solution digestion Off-line HPLC-RP Basic pH Methanol/Chloroform precipitation In-solution digestion Off-line.
Which of the following statements is the most correct? 1.Viral envelopes contain both viral and host proteins 2.Viral envelopes contain glycoproteins for.
Transcription begins - Cell gets message that a protein needs to be made & a portion of DNA unwinds exposing the gene that needs to be copied.
Spectral Counting. 2 Definition The total number of identified peptide sequences (peptide spectrum matches) for the protein, including those redundantly.
Determining the Number of Non- Spurious Arcs in a Learned DAG Model: Investigation of a Bayesian and a Frequentist Approach Listgarten & Heckerman.
Facts and Fallacies about de Novo Sequencing & Database Search.
Breadth First Search
Your blood type is established before you are BORN, by specific GENES inherited from your parents. These two genes - one gene from your MOTHER and one.
Virginia G. Piper Center for Personalized Diagnostics Chromosome 10 Joshua LaBaer, M.D., Ph.D. Konstantinos Petritis, Ph.D. Virginia G. Piper Center for.
MRNA attaches to ribosome in cytoplasm tRNA moves towards mRNA to deliver its amino acid Amino acids link up to form a protein. A peptide bond links two.
1 Amide Bond Formation Amide bonds form upon reaction of carboxylic acids with ammonia, primary amines or secondary amines. When amide bonds form between.
Peptidesproteinsgenes protein accessionsharedsharedunique gene nameshareduniqueunique Identified by gene unique peptides Identified by protein and gene.
9.6 Genetic Screening and Gene Therapy KEY CONCEPT Genetics provides a basis for new medical treatments.
TICKET REQUIRED FOR ENTRY: A completed, up to date LO booklet THE WONDERFUL WORLD OF ENZYMES.
False-Discovery-Rate Aware Protein Inference by Generalized Protein Parsimony Nathan Edwards Department of Biochemistry and Molecular & Cellular Biology.
Mutational analysis of 35 bladder cancer cell lines using RNA-seq.
20,000 GENES IN HUMAN GENOME; WHAT WOULD HAPPEN IF ALL THESE GENES WERE EXPRESSED IN EVERY CELL IN YOUR BODY? WHAT WOULD HAPPEN IF THEY WERE EXPRESSED.
SRM working plan. La Cristalera, 5-6 November 2013.
Getting Started 1. Write the complementary strand for the following: 5’ – TGACTTGACGGA – 3’ 2. We are born looking exactly like our parents. True.
PROTEIN SYNTHESIS PART 2 AP BIOLOGY. PEPTIDE BONDING.
AP Biology Protein Synthesis Part 2. Peptide Bonding.
Common parameters At the beginning one need to set up the parameters.
Analysis of Complex Proteomic Datasets Using Scaffold Free Scaffold Viewer can be downloaded at:
A New Strategy of Protein Identification in Proteomics Xinmin Yin CS Dept. Ball State Univ.
From Genome to Proteome Juang RH (2004) BCbasics Systems Biology, Integrated Biology.
“Hotspot” algorithm chr5:131,975, ,012,092 Idea: gauge enrichment of tags relative to a local background model based on the number of tags in a 50kb.
Notes - DNA, Genes, and Chromosomes. Cells and DNA All organisms are made of one or more cells All organisms are made of one or more cells With few exceptions,
CISC667, F05, Lec9, Liao CISC 667 Intro to Bioinformatics (Fall 2005) Sequence Database search Heuristic algorithms –FASTA –BLAST –PSI-BLAST.
Data Standards Submission 1 st CHr-16 Workshop. Miraflores de la Sierra August, 28 th -29 th 2012 Alberto Medina.
Statistical Testing with Genes Saurabh Sinha CS 466.
Bioinformatic Investigation of Insulin Signalling System.
Identification of thioredoxin h targets in guard cell enriched epidermal peels using cysTMT proteomics Tong Zhang, Ph.D. Department of Biology University.
Today in Lab: In Search of the Sickle Cell Gene. A Simple Mutation With a Profound Impact.
RNA Makin’ Proteins DNAMutations Show off those Genes!
Protein Sequencing and Identification by Mass Spectrometry.
Transcription and Translation… Its what make you, YOU!
EXTRACTION AND FINGERPRINTING DNA. The Genetic Code Genes- control the production of proteins in an organisms cells. Proteins determine the traits of.
Central Dogma (for your disease?) LB 145 February 22-23, 2011.
Name of the topic Author, group, General information about protein (we suggest to use the websites
Introduction to Oral Cancer Gene Database ．資訊三 朱民晃 B ．資訊三 陳皓遠 B
Video Questions What do the following prefixes mean? Mono, Poly, Exo, and End What do you need to have “LIFE”? Draw a picture of an atom. Why do atoms.
Chapter 22 (Part 2) Protein Synthesis. Ribosomes.
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