Signaling Pathways and Summary
June 30, 2005
Signaling lecture
Course summary
Tomorrow
Next Week Friday, 7/8/05 Morning presentation of writing
assignments. Evals of faculty.
What is signal transduction?
Conversion of a signal from one physical or chemical form into another.
In cell biology, commonly refers to the sequential process initiated by binding of an extracellular signal to a receptor and culminating in one or more specific cellular responses.
What is a signal transduction pathway?
ABCDEFG
Chemical signals are converted from one type of signalinto another to elicit a molecular response from the organism.All organisms require signaling pathways to live.
Letters represent chemicals or proteins. Arrows representenzymatic steps.
What is a second messenger?
An intracellular signaling molecule whose concentration increases (or decreases) in response to binding of an extracellular ligand to a cell-surface receptor.
Seven levels of regulation of cell growth
Signal Transduction Animations
http://www.celanphy.sci.kun.nl/Bruce%20web/Flash%20Movies.htm
Database to deal with signaling pathways (still in development)
http://www.grt.kyushu-u.ac.jp/spad/index.html
KEGG
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for understanding higher order functional meanings and utilities of the cell or the organism from its genome information. The KEGG project is undertaken in the Bioinformatics Center, Institute for Chemical Research, Kyoto University with supports from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), the Japan Society for the Promotion of Science (JSPS), and the Japan Science and Technology Corporation (JST).
Databases of KEGG
Metabolic pathways http://www.genome.ad.jp/kegg/kegg2.html - pathway
Regulatory pathways
Ortholog tables
Other Signaling Pathway Links
http://david.niaid.nih.gov/david/Links-Pathways.htm
http://sugp.caltech.edu/endomes/
Goals of SoCalBSI
1) Bioinformatics software programs
2) Programming
3) Explore ethical issues
4) Future careers
5) Research experiences
6) Interactions with professional bioinformaticists
7) Foster long-lasting professional relationships
Core BioinformaticsLiterature SearchingNCBI ModelScoring MatricesDynamic ProgrammingGlobal vs. Local Sequence AlignmentMultiple Sequence AlignmentPhylogenetic TreesMolecular Life Science DatabasesProtein ModelingMicroarraysProteomics
EthicsPrivacySecurityHuman Genome
MolecularLife Science
Central DogmaMolecular Basis of DiseaseDNA Primary SequenceProtein Primary, Secondary, Tertiary StructureMolecular EvolutionSignal Transduction
Computer ScienceStructured ProgrammingData StructuresAlgorithmsComplexity AnalysisSoftware Engineering
StatisticsProbability TheoryHidden Markov ChainBayes’ TheoryExpect ValueRule of Counting
Course SummaryProgram Learning Objectives (partial list):
Retrieve gene sequence information from GenBank and Protein databasesUse BLAST program to conduct gene similarity searchesAlign multiple sequences with Clustal W programPredict protein functional motifs with BLIMPs Display and compare 3-D structures of proteinsModel protein structure using a homologous structure analysis program (Deep View)Write algorithms that will perform a simple searches of gene sequences stored in a database or perform pairwise alignmentsUnderstand the statistics used in scoring aligned sequences in common programs.Appreciate the ethical issues that developed from sequencing the human genome.
List of software programs you should be familiar with
PubMedDotterNeedleman-Wunsch global alignmentSmith-Waterman local alignmentBLASTFASTAPhylipMascot/ProteinProspector
ChouFasmanKyte-DoolittleGORCLUSTAL WBLIMPsPSIPREDDeepView (Swiss PDB viewer)
List of databases that we studied
Online Mendelian Inheritance of Man
MedLine
GenBank
EMBL
SWISSPROT
Protein Information Resource
ProSite
BLOCKS
Protein Data Bank (PDB)
Swiss 2D Gel
KEGG
Concepts in bioinformatics
ENTREZ-Suite of connected programs that allow for analysis of genes and proteinsModular nature of proteinsSliding windowAlignment methods (Local vs. Global)Dynamic programmingStatistics (E-value, Z-score, Probabilities, Bayes’ Theorem)
Concepts in bioinformatics II
Primary and secondary databasesSimilarity vs. identical amino acidsScoring matrices (PAM, BLOSUM, PSSM)Multiple alignmentGuide treesNeural networksProtein structure predictionDeveloping software program that aligns sequences based on scoring matrices
Future of bioinformatics
Traditionally divided into two camps-users and developers
SoCalBSI students should have an advantage over the typical applicant to graduate school or industry position
Online Journal of Bioinformatics
Bio Inform-a newsletter for bioinformaticists
Systems Biology