Advanced bioinformatics methods for proteomics
Upcoming SlideShare
Loading in...5
×
 

Advanced bioinformatics methods for proteomics

on

  • 547 views

 

Statistics

Views

Total Views
547
Views on SlideShare
474
Embed Views
73

Actions

Likes
0
Downloads
10
Comments
0

1 Embed 73

http://www.scoop.it 73

Accessibility

Categories

Upload Details

Uploaded via as Microsoft PowerPoint

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment

Advanced bioinformatics methods for proteomics Advanced bioinformatics methods for proteomics Presentation Transcript

  • Advanced bioinformaticsmethods for proteomics Lars Juhl Jensen
  • three parts
  • signaling networks
  • association networks
  • text mining
  • Part 1signaling networks
  • phosphoproteomics
  • Linding, Jensen, Ostheimer et al., Cell, 2007
  • in vivo phosphosites
  • kinases are unknown
  • sequence specificity
  • Miller, Jensen et al., Science Signaling, 2008
  • NetPhorest
  • Miller, Jensen et al., Science Signaling, 2008
  • motif atlas
  • kinases
  • phospho-binding proteins
  • phosphatases
  • protein-specific
  • no context
  • co-activators
  • protein scaffolds
  • localization
  • expression
  • association network
  • Linding, Jensen, Ostheimer et al., Cell, 2007
  • NetworKIN
  • Linding, Jensen, Ostheimer et al., Cell, 2007
  • web interface
  • Part 2association networks
  • guilt by association
  • STRING
  • Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
  • >1100 genomes
  • computational predictions
  • genomic context
  • gene fusion
  • Korbel et al., Nature Biotechnology, 2004
  • phylogenetic profiles
  • Korbel et al., Nature Biotechnology, 2004
  • experimental data
  • physical interactions
  • Jensen & Bork, Science, 2008
  • gene coexpression
  • curated knowledge
  • pathways
  • Letunic & Bork, Trends in Biochemical Sciences, 2008
  • many databases
  • different formats
  • different identifiers
  • variable quality
  • not comparable
  • quality scores
  • von Mering et al., Nucleic Acids Research, 2005
  • calibrate vs. gold standard
  • von Mering et al., Nucleic Acids Research, 2005
  • missing most of the data
  • Part 3text mining
  • >10 km
  • too much to read
  • computer
  • as smart as a dog
  • teach it specific tricks
  • named entity recognition
  • comprehensive lexicon
  • proteins
  • cellular components
  • compartments.jensenlab.org
  • tissues
  • tissues.jensenlab.org
  • diseases
  • orthographic variation
  • singular vs. plural
  • spaces and hyphens
  • “black list”
  • information extraction
  • co-mentioning
  • NLPNatural Language Processing
  • Gene and protein namesCue words for entity recognitionVerbs for relation extraction[nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]] is controlled by [nxpg HAP1]
  • summary
  • bioinformatics
  • more than BLAST
  • data/text mining
  • save you much time
  • AcknowledgmentsNetPhorest NetworKIN STRING Text-Rune LindingMartin Lee Miller Rune Linding Heiko Horn Christian von Mering Damian Szklarczyk miningErwin Schoof Gerard Ostheimer Michael Kuhn Sune FrankildFrancesca Diella Martin Lee Miller Manuel Stark Evangelos PafilisClaus Jørgensen Francesca Diella Samuel Chaffron Janos BinderMichele Tinti Karen Colwill Chris Creevey Heiko HornLei Li Jing Jin Jean Muller Michael KuhnMarilyn Hsiung Pavel Metalnikov Tobias Doerks Nigel BrownSirlester A. Parker Vivian Nguyen Philippe Julien Reinhardt SchneiderJennifer Bordeaux Adrian Pasculescu Alexander Roth Sean O’DonoghueThomas Sicheritz-Pontén Jin Gyoon Park Milan SimonovicMarina Olhovsky Leona D. Samson Jan KorbelAdrian Pasculescu Rob Russell Berend SnelJes Alexander Peer Bork Martijn HuynenStefan Knapp Michael Yaffe Peer BorkNikolaj Blom Tony PawsonPeer BorkShawn LiGianni CesareniTony PawsonBenjamin E. TurkMichael B. YaffeSøren Brunak
  • larsjuhljensen