Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project....
-
date post
18-Dec-2015 -
Category
Documents
-
view
216 -
download
0
Transcript of Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project....
![Page 1: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/1.jpg)
Bioinformatics and ChipsBioinformatics and Chips
Bioinformatics is a very Bioinformatics is a very integral part of each step in integral part of each step in a chip project.a chip project.
![Page 2: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/2.jpg)
Steps in a Chip ProjectSteps in a Chip Project
1 Biological question2 Design experiment3 Design chip4 Run experiment5 Read out chip6 Treat data7 Biological answer
First overview, then details
![Page 3: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/3.jpg)
Biological QuestionBiological Question
A chip experiment is only worth doing, if it answers a question that is worth asking.
![Page 4: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/4.jpg)
Design ExperimentDesign Experiment
Not every question can be answered with a chip experiment.
Some questions that can be answered with a chip experiment can also be answered with another (cheaper) experiment.
![Page 5: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/5.jpg)
Design experimentDesign experiment
Probes on the chip:
UniqueReproducible
![Page 6: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/6.jpg)
Run ExperimentRun Experiment
Like every binding study, chip experiments have a thermodynamic and a kinetic component.
![Page 7: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/7.jpg)
Run ExperimentRun Experiment
Binding thermodynamics:
G = H - TSG = - R T ln(K)
G = 1.4 kCal/M ~ Factor 10 in K1 H-bond ~ 1 – 4 kCal/M
![Page 8: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/8.jpg)
Chip Read Out is ‘Solved’Chip Read Out is ‘Solved’
And, what is more, it has nothing to do with bioinformatics.
![Page 9: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/9.jpg)
Treat DataTreat Data
I assume this has been discussed in other sessions in this course.
![Page 10: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/10.jpg)
Biological AnswerBiological Answer
This is not just bioinformatics.Everything you know can, and should, be used at this stage.
![Page 11: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/11.jpg)
Knowledge neededKnowledge needed
No matter what chip-array software you use, you will want to know all there is to know about the genes/proteins that are on the chip. So, up-to-date databases are always needed.
![Page 12: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/12.jpg)
Some toolsSome tools
BLASTSRSKEGG
www.cmbi.kun.nl
![Page 13: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/13.jpg)
BLASTBLAST
![Page 14: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/14.jpg)
BLASTBLAST
![Page 15: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/15.jpg)
BLASTBLAST
![Page 16: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/16.jpg)
BLASTBLAST
![Page 17: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/17.jpg)
SRSSRS
![Page 18: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/18.jpg)
SRSSRS
![Page 19: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/19.jpg)
SRSSRS
![Page 20: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/20.jpg)
SRSSRS
![Page 21: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/21.jpg)
SRSSRS
![Page 22: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/22.jpg)
KEGGKEGG
![Page 23: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/23.jpg)
KEGGKEGG
![Page 24: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/24.jpg)
KEGGKEGG
![Page 25: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/25.jpg)
KEGGKEGG
![Page 26: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/26.jpg)
KEGGKEGG
![Page 27: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/27.jpg)
KEGGKEGG
![Page 28: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/28.jpg)
SwissProtSwissProt
ID CRAM_CRAAB STANDARD; PRT; 46 AA.
AC P01542;
DT 21-JUL-1986 (Rel. 01, Created)
DT 21-JUL-1986 (Rel. 01, Last sequence update)
DT 01-NOV-1997 (Rel. 35, Last annotation update)
DE CRAMBIN.
GN THI2.
OS Crambe abyssinica (Abyssinian crambe).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC euphyllophytes; Spermatophyta; Magnoliophyta; eudicotyledons;
OC core eudicots; Rosidae; eurosids II; Brassicales; Brassicaceae;
OC Crambe.
![Page 29: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/29.jpg)
SwissProtSwissProt
RN [1]RP SEQUENCE.RX MEDLINE; 82046542.RA TEETER M.M., MAZER J.A., L'ITALIEN J.J.;RT "Primary structure of the hydrophobic plant protein crambin.";RL Biochemistry 20:5437-5443(1981).
CC -!- FUNCTION: THE FUNCTION OF THIS HYDROPHOBIC PLANTCC SEED PROTEIN IS NOT KNOWN.CC -!- SIMILARITY: BELONGS TO THE PLANT THIONIN FAMILY.
DR PIR; A01805; KECX.DR PDB; 1CRN; 16-APR-87.DR PDB; 1CBN; 31-JAN-94.
![Page 30: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/30.jpg)
SwissProtSwissProt
FT DISULFID 3 40FT DISULFID 4 32FT DISULFID 16 26FT VARIANT 22 22 P -> S.FT VARIANT 25 25 I -> L.FT STRAND 2 3FT HELIX 7 16FT TURN 17 19FT HELIX 23 30FT TURN 31 31FT STRAND 33 34FT TURN 42 43SQ SEQUENCE 46 AA; 4736 MW; F6ADE458 CRC32;>P1;CRAM_CRAAB
TTCCPSIVAR SNFNVCRLPG TPEAICATYT GCIIIPGATC PGDYAN*
![Page 31: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/31.jpg)
SignificanceSignificance
![Page 32: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/32.jpg)
PointersPointers
www. cmbi.kun.nl/www. cmbi.kun.nl/srs/www. cmbi.kun.nl/bioinf/tools/blast.shtmlwww. genome.ad.jp/kegg/www. affymetrix.com/www. dmd.nl/arrayNL/arrayNL.htmlwww. gene-chips.com/
(the blank in there is not real, but needed if you use this Windows thing)
![Page 33: Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in.](https://reader036.fdocuments.in/reader036/viewer/2022062421/56649d235503460f949f9793/html5/thumbnails/33.jpg)
PointersPointers
www. BioASP.nlBioinformatica.pagina.nljura.ebi.ac.uk:8765/gqsrv/submitSoon an CMBI/BioASP: Pedant
(the blank in there is not real, but needed if you use this Windows thing)