statistics for microarrays
DESCRIPTION
Statistics for Microarrays. Biological background: Molecular Biology. Class web site: http://statwww.epfl.ch/davison/teaching/Microarrays/. Acknowledgements. http://www.accessexcellence.org/AB/GG http://www.oup.co.uk/best.textbooks/biochemistry/genesvii - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/1.jpg)
Biological background: Molecular Biology
Class web site: http://statwww.epfl.ch/davison/teaching/Microarrays/
Statistics for Microarrays
![Page 2: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/2.jpg)
Acknowledgements
• http://www.accessexcellence.org/AB/GG•http://www.oup.co.uk/best.textbooks/biochemistry/genesvii• Sandrine Dudoit, UC Berkeley Biostatistics• Yee Hwa Yang, UC Berkeley Statistics• Terry Speed, UC Berkeley Statistics and WEHI, Melbourne, Australia
![Page 3: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/3.jpg)
Two types of organisms*
* Every biological ‘rule’ has exceptions!
![Page 4: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/4.jpg)
Timeline of Genetics Highlights
![Page 5: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/5.jpg)
http://www.stg.brown.edu/webs/MendelWeb/MWtoc.html
Mendelian Genetics
![Page 6: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/6.jpg)
Human Chromosomes
![Page 7: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/7.jpg)
Human Chromosome Banding Patterns
![Page 8: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/8.jpg)
Chromosomes and DNA
![Page 9: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/9.jpg)
Cell Division -- Mitosis
![Page 10: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/10.jpg)
Cell Division -- Meiosis
![Page 11: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/11.jpg)
Crossing over and Recombination
![Page 12: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/12.jpg)
Mitosis and Meiosis Compared
![Page 13: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/13.jpg)
(BREAK)
![Page 14: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/14.jpg)
Nature (1953), 171:737
“We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest.”
DNA Structure Discovery
![Page 15: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/15.jpg)
DNA
• A deoxyribonucleic acid or DNA molecule is a double-stranded linear polymer composed of four molecular subunits called nucleotides
• Each nucleotide comprises a phosphate group, a deoxyribose sugar, and one of four nitrogen bases: adenine (A), guanine (G), cytosine (C), or thymine (T)
• The two strands are held together by weak hydrogen bonds between complementary bases
• Base-pairing occurs according to the rule: G pairs with C, and A pairs with T
![Page 16: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/16.jpg)
DNA A-type (140D)(low water content)
DNA B-type (7BNA)(Watson-Crick form)
DNA Z-type (2ZNA)(high salt concentration)
Polymorphic DNA Tertiary Structures
![Page 17: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/17.jpg)
Genes are linearly arranged along chromosomes
![Page 18: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/18.jpg)
DNA Structure (overview)
![Page 19: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/19.jpg)
A nucleotide is a phospate, a sugar, and a purine (A, G) or a pyramidine (T, C) base.
The monomeric units of nucleic acids are called nucleotides.
DNA Structure
![Page 20: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/20.jpg)
Adenine (A) Guanine (G) (Purines)
Thymine (T) (DNA) (Pyrimidines)
Cytosine (C)
Uracil (U) (RNA)
Nucleotide Bases
![Page 21: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/21.jpg)
Nucleotide codesA Adenine W Weak (A or T)
G Guanine S Strong (G or C)
C Cytosine M Amino (A or C)
T Thymine K Keto (G or T)
U Uracil B Not A (G or C or T)
R Purine (A or G) H Not G (A or C or T)
Y Pyrimidine (C or T) D Not C (A or G or T)
N Any nucleotide V Not T (A or G or C)
![Page 22: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/22.jpg)
Base Pairing
![Page 23: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/23.jpg)
Proteins
• Proteins: macromolecules composed of one or more chains of amino acids
• Amino acids: class of 20 different organic compounds containing a basic amino group (-NH2) and an acidic carboxyl group (-COOH)
• The order of amino acids is determined by the base sequence of nucleotides in the gene coding for the protein
• Proteins function as enzymes, antibodies, structures, etc.
![Page 24: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/24.jpg)
Amino acid codesAlaArgAsnAspCysGlnGluGlyHisIleLeuLysMetPheProSerThrTrpTyrVa lAsxGlxSecUnk
ARNDCQEGHILKMFPSTWYVBZUX
AlanineArginineAsparagineAspartic acidCysteineGlutamineGlutamic acidGlycineHistidineIsoleucineLeucineLysineMethioninePhenylalanineProlineSerineThreonineTryptophanTyrosineValineAsn or AspGln or GluSelenocysteineUnknown
![Page 25: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/25.jpg)
Primary Protein Structure
![Page 26: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/26.jpg)
Multiple Levels of Protein Strucure
( Protein folding)
![Page 27: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/27.jpg)
Tertiary Structure ofSperm whale myoglobin (1MBN)
![Page 28: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/28.jpg)
![Page 29: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/29.jpg)
(RT)
![Page 30: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/30.jpg)
Nature (1953), 171:737
“It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”
DNA Replication
![Page 31: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/31.jpg)
![Page 32: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/32.jpg)
DNA Replication
• The DNA strand that is copied to form a new strand is called a template
• In the replication of a double-stranded or duplex DNA molecule, both original (parental) DNA strands are copied
• When copying is finished, the two new duplexes, each consisting of one of the original strands plus its copy, separate from each other (semiconservative replication)
![Page 33: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/33.jpg)
Semiconservative Replication
![Page 34: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/34.jpg)
DNA Replication, ctd• DNA synthesis occurs in the chemical direction 5’3’• Nucleic acid chains are assembled from 5’ triphosphates of
deoxyribonucleosides (the triphosphates supply energy)• DNA polymerases are enzymes that copy (replicate) DNA• DNA polymerases require a short preexisting DNA strand
(primer) to begin chain growth. With a primer base-paired to the template strand, a DNA polymerase adds nucleotides to the free hydroxyl group at the 3’ end of the primer.
• DNA replication requires assembly of many proteins (at least 30) at a growing replication fork: helicases to unwind, primases to prime, ligases to ligate (join), topisomerases to remove supercoils, RNA polymerase, etc.
![Page 35: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/35.jpg)
![Page 36: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/36.jpg)
DNA Replication Fork
![Page 37: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/37.jpg)
DNA is unwinding
DNA Synthesis
![Page 38: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/38.jpg)
![Page 39: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/39.jpg)
![Page 40: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/40.jpg)
RNA• RNA, or ribonucleic acid, is similar to DNA, but
-- RNA is single-stranded-- the sugar is ribose rather than
deoxyribose-- uracil (U) is used instead of thymine
• RNA is important for protein synthesis and other cell activities
• There are several classes of RNA molecules, including messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and other small RNAs
![Page 41: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/41.jpg)
The Genetic Code
• DNA: sequence of four different nucleotides
• Protein: sequence of twenty different amino acids
• The correspondence between the four-letter DNA alphabet and the twenty-letter protein alphabet is specified by the genetic code, which relates nucleotide triplets, or codons, to amino acids
![Page 42: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/42.jpg)
Standard Genetic Code
![Page 43: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/43.jpg)
Variation of genetic codesT1 T2 T3 T4 T5 T6 T9 T10 T12 T13 T14 T15
CUUCUCCUACUG
LeuLeuLeuLeu
----
ThrThrThrThr
----
----
----
----
----
---Ser
----
----
----
AUUAUCAUAAUG
IleIleIleMet
--Met-
--Met-
----
--Met-
----
----
----
----
--Met-
----
----
UAUUACUAAUAG
TyrTyrStopStop
----
----
----
----
--GlnGln
----
----
----
----
--Tyr-
---Gln
AAUAACAAAAAG
AsnAsnLysLys
----
----
----
----
----
--Asn-
----
----
----
--Asn-
----
UGUUCGUGAUGG
CysCysStopTrp
--Trp-
--Trp-
--Trp-
--Trp-
----
--Trp-
--Cys-
----
--Trp-
--Trp-
----
AGUAGCAGAAGG
SerSerArgArg
--StopStop
----
----
--SerSer
----
--SerSer
----
----
--GlyGly
--SerSer
----
T1: standardT2: vert mtT3: yeast mtT4: other mtT5: invert. mtT6: cil. etc nuc.T9: ech. mtT10: eup. nuc.T12:alt yeast nucT13: asc. mtT14: flat. mtT15: bleph. nuc.
![Page 44: Statistics for Microarrays](https://reader033.vdocuments.site/reader033/viewer/2022042901/56813e40550346895da825e2/html5/thumbnails/44.jpg)
Protein Synthesis