【KNOWLEADGE】Gene Function Analysis

linxingxing

With the advent of high-throughput technologies, the number of genes of interest has expanded and the traditional methods for gene function analysis cannot achieve the throughput necessary for large-scale exploration. In Gene Function Analysis, a select team of experts bring together a number of recently developed techniques for studying gene function.  The volume begins with a variety of computational techniques, which provide an excellent point of departure for the cutting-edge experimental methods that follow.  Written in the highly successful Methods in Molecular Biology™ series format, each chapter surveys its subject with readily reproducible laboratory protocols, a list of the necessary materials, and the popular Notes section, which contains tips for troubleshooting and avoiding known pitfalls.
- W- S' P1 v7 r
6 o, `0 O0 p4 N3 cComprehensive and timely, Gene Function Analysis offers researchers a clear guide and the important tools they need to further study the intricate human genome.% e" U2 a( O4 A( X/ f

7 f9 m0 C5 I- {: V! j( I: b3 n. KContent Level » Research
* V, X$ b% S7 _7 O8 y, f/ z& ^! h
: n) S( ^- R: S. K) g% NRelated subjects » Bioinformatics - Biotechnology - Cell Biology - Human Genetics
2 E& q( T1 U( k$ c' e! |% c
; T, M* l( j: }( u" uTable of contentstableOfContents
! ~/ \5 V5 o2 P7 K- Y$ OMethods in Molecular Biology: Gene Function Analysis
5 \# d6 Q1 w* q0 a
' B5 h4 a0 ~) Y7 b) hTable of Contents& j, r* \, A# U
0 T* H7 \- H: n. d, b, s. p
8 _4 \3 }7 c, X+ s! B* o0 N* U
Computational Methods I; o! g! }. I" P) q. Z/ N6 O* ]
+ J) Q' x( Y: M
1 Gene function inference from gene expression of deletion mutants% W8 I( w/ Q. m9 M% @0 [
Ghislain Bidaut% y: s% Y# r/ }) z  [
  E9 a; f  t" Z" g8 S5 `& @8 J
2 Association analysis for large scale gene set data$ ]/ r1 ?: y' c8 `" q7 d; Y/ i
Stefan Kirov, Bing Zhang, Jay Snoddy2 P. J* `5 |! o3 X
& z/ |( M8 T3 a) T
3 Estimating Gene Function with Least Squares Nonnegative Matrix% B# E! M0 g, o; Y5 G; Y5 `  G
Factorization
- g! c5 q& J1 uGuoli Wang and Michael F. Ochs9 e  ^% ]. N6 _% N. f9 H
$ d' `. Z) P6 b0 N6 U2 b
4 From Promoter Analysis to Transcriptional Regulatory Network
* Q2 I$ J0 s! }+ [' k( G5 SPrediction Using PAINT: f) i% G0 A& v' v0 C
Gregory E. Gonye, Praveen Chakravarthula, James S. Schwaber,$ W% k, d  Z  j/ j, c
Rajanikanth Vadigepalli
, d/ W1 ~# d/ E* \& `
3 ?. E7 J3 l4 B; _5 Prediction of Intrinsic Disorder and its Use in Functional Proteomics
, g7 M$ J6 g  M! j. _Vladimir N. Uversky, Predrag Radivojac, Lilia M. Iakoucheva, Zoran
% X9 \/ e# b/ `4 N2 e7 d9 G7 GObradovic, A. Keith Dunker
. z$ `+ }4 {! d7 _/ E3 f- X- }# @2 S( `
2 ~' A' Z% P1 h$ Q1 |6 X; \1 X3 f8 E. o
Computational Methods II8 l( f8 p2 Y2 j2 y* H% V

% }. V/ Z3 I1 U/ Z& R6 Sybil: Methods and Software for Multiple Genome Comparison and
. a# ]% s( v# X. \$ j, ^5 @Visualization
, J$ Q, Y8 w) _) w  jJonathan Crabtree, Samuel V. Angiuoli, Jennifer R. Wortman, Owen White, m* Z' Z8 g- I2 @- K+ W

0 m+ Y* O7 \6 S7 Estimating protein function using protein-protein relationships4 _' n6 k+ y: @4 Y, q
Shailesh V. Date
# n. k# H! o4 C  m. q
( s2 r6 F3 J# g$ L$ i. w, Q  P3 F8 Bioinformatics tools for modeling transcription factor target genes
6 g" U# D/ v/ n: H( u6 Land epigenetic changes
% V% O# k+ L9 S( ^% E& i$ `, iRamana V. Davuluri" b1 l% i0 w) r  S2 R* Z0 Q

* d/ i3 v1 R/ Q  c" d6 N9 Mining Biomedical Data Using MetaMap Transfer (MMTx) and the Unified( a# h6 K: N8 ]
Medical Language System (UMLS)
' W  Z) |6 C: L2 f9 zJohn D. Osborne, Simon Lin, Lihua (Julie) Zhu, Warren A. Kibbe1 L. a: c: i8 v+ v
' X) L% H* l  u! t4 o
10 Statistical Methods for Identifying Differentially Expressed Gene
! P6 W/ P9 s: nCombinations
. \2 D- B- D- l8 GYen-Yi Ho, Leslie Cope, Marcel Dettling, Giovanni Parmigiani
' l0 N/ }: e6 b2 f' c+ A
* l. {. ]# @! e/ f- L3 g1 |
$ |, ~7 F# S+ h' e& f* eExperimental Methods
- _/ X6 J$ l" j7 V1 z" r
' Q6 M+ k6 H2 U( v9 i: p1 R, U. i11 Gene Function Analysis using the chicken B-cell Line DT403 W3 N/ _$ \$ c2 A" k  h
Randolph B Caldwell, Petra Fiedler, Ulrike Schoetz and Jean-Marie
4 {  ]! g( b' D) Q) n4 a6 @1 u* b4 ABuerstedde
: W4 r) W, F) \
$ J) s$ |4 s3 z% I# ?9 C( ?* c12 Design and application of an shRNA-based gene replacement retrovirus.8 V8 ?! u) q: U: |, f* g( s
Rugang Zhang, Peter D. Adams and Xiaofen Ye
. r: G0 F" U/ v5 J! ~" B+ _
8 I! L: m: \$ o0 P# V3 @" ^13 Construction of simple and efficient DNA vector-based short hairpin% T3 \1 A- ?' a
RNA
% @) }. ^" v( ^5 D" Gexpression systems for specific gene silencing in mammalian cells3 }' c4 H3 _- v6 [" h
Tsung-Lin Cheng a and Wen-Tsan Chang. y/ v! \1 m& X: Q+ q, n* ~4 W7 y
1 Z0 p9 J' u2 J# m5 L
14 Selection of recombinant antibodies from antibody gene libraries
, A2 g; L, i. i" tMichael Hust, Stefan Dübel and Thomas Schirrmann! g* E( D- l6 j2 d9 e

) @- H1 Z( t- U% Z  }" T2 {# }15 A bacterial/yeast merged two-hybrid system: protocol for yeast2 ?: g2 {( E. w0 R  G$ ~+ c
screening with single or parallel baits.
0 r$ l1 n  K/ p$ K) D& ]Nadezhda Tikhmyanova, Eugene Izumchenko, Ilya G. Serebriiskii, Erica A.1 s( m  c  Y9 Q; h, S* _0 _- T0 b6 I
Golemis
' y1 B& k& o$ x' m2 v4 J0 }, K, x- s8 k
16 A bacterial/yeast merged two-hybrid system: protocol for bacterial
+ v" n. q' x3 }' K* l/ Hscreening1 m' W5 d0 t% E, g( \
Ilya G. Serebriiskii, Nadia Milech, Erica A. Golemis
( z' S: q6 l8 c0 C
2 ^4 \  R6 _: f! j6 I17 Engineering Cys2His2 Zinc Finger Domains using a Bacterial; Z% Q$ o% v/ b1 o$ z
Cell-Based Two-Hybrid Selection System
  n- R9 |5 Y  gStacey Thibodeau-Beganny and J. Keith Joung

linxingxing

Functional Analysis Program
* b. i# n& D: G6 X) gOverview
  C, q5 r9 v3 ?, ]Research Objectives 7 `1 O+ {  h3 N6 |  |
Policies, Reports and Related Project Information 2 y# \9 M( M* d3 B$ \
Funding Opportunities
3 `' s8 H4 k$ qStaff ) l' D9 t5 B9 @9 R
; Q5 t/ @7 u. W  m3 o8 k
% f2 Z( i0 a! [3 L5 H

6 z; W/ N  e0 r- l* ]6 `+ t9 x, U0 E
Functional Analysis Program Overview
5 Z2 q$ b1 r% |# |Completely sequencing an organism's genome is just the beginning of our understanding of that organism's biology. All of the genes still need to be identified; the function of those genes' expressed products (functional RNAs and proteins) must be elucidated; and the non-coding regulatory sequences need to be understood. The Functional Analysis of the Genome program manages and supports research that will lead to improved techniques and strategies for efficient identification and functional analysis of genes, coding regions and other functional elements of entire genomes on a high throughput basis.% A* N3 r& b& C+ Z- l* Q2 M

3 H) V& H" i# o! s+ [0 P+ Z5 Q+ r( h# qThe main emphasis of this program is technology development. These technologies must be efficient, robust and have the potential to be applied in a large-scale yet cost-effective manner. The program also supports the large-scale application of high-throughput and efficient technologies on a limited basis, primarily in model organisms. (The application of these technologies to specific, highly focused biological or medical problems is not supported under this program).) i3 m2 h* x% Q% h4 }- t  ]& |2 M

# m; c) A2 Y$ t0 y" l4 R5 HTop of page
; P+ Y8 c5 m1 r9 D' O$ v
9 h8 e# f0 [4 ?: \! M9 c8 P$ tFunctional Analysis Program Research Objectives: 6 ]  U$ |* R" A/ M9 E0 A
Identification and mapping of all functional elements (both coding and non-coding) in a genome./ d5 B, Y  m$ t# C% b- ~

; X5 }, Q) S. P8 ]# N, a: B1 K$ k$ x% ?8 `: K) k" H. k
Generation of high-quality, full-length and representative cDNA libraries.- d$ {3 T  o8 P+ c( [. ~

) J# I" [0 `. i% t; Y
& U6 J0 O6 r/ IAnalysis of steady-state RNA and protein expression levels in a given cell type; of comparative levels of gene products in different cell types; and of temporal or induced changes in RNA and protein expression.
3 I: w& y1 i# a/ L" y) q8 l3 W+ e, b% C7 T5 m6 y

6 l& B& `& Q2 q0 [+ GAnalysis of naturally occurring or induced mutations that alter RNA and/or protein expression.* c+ T/ Z, g& ?6 r/ R3 k& s7 K

8 c- m2 x. q% @3 k; ^5 D
: }/ T/ s: i# ~: T* J/ K; sAnalysis of cellular localization of proteins and of protein-protein, or protein-nucleic acid, interactions.+ i' _1 B2 N7 ]) W) J! U3 e

7 L1 M- J* L" _1 q
& X; z6 F0 D; n' ?5 f8 NComparative analysis of protein sequences.& K/ u/ u. d1 o
- T$ i. a; {, e

! c4 N% l" S+ {/ s3 ?Analysis of genome organization and its effect on cellular functions.
+ i: {3 S* l2 X+ D1 x2 W7 J+ |8 `/ t, }' p% ?6 K
. E* I/ ]2 W! z$ q: K$ b7 z1 m
Top of page
3 c" j( K* R/ M( ?# R4 V
: c4 {5 T; @6 XFunctional Analysis Program Policies, Reports and Related Program Information/ |0 w8 L" S; `
Workshop Reports
  x/ J$ d. r2 H  PWorkshop on the Comprehensive Extraction of Biological Information from Genomic Sequence July 23 - 24, 2002
1 f+ @1 A/ i! g, b1 Z& X
9 s5 G8 `5 X4 K9 V2 UNon-Mammalian Models Workshop [nih.gov] February 16-17, 1999# w) O  ~/ s# u
, O+ f. |3 j# q! r0 v* I# t. b
Functional Analysis Workshop December 2-3, 1997- V3 z( ]! K9 t0 G5 ~' P: Z3 d
4 R$ j0 L" p5 n* @  d
Related Projects
7 G7 p6 O& z- f0 U% Q0 f: ?/ w3 ^ENCODE (Encyclopedia of DNA Elements)
6 j% I3 ~8 {4 b9 [" G+ H4 L: Z$ zThe long-term goal of the ENCODE project is to identify all functional elements in the human genome sequence. For use in a pilot project, defined regions of the human genome - corresponding to 30Mb, roughly 1 percent - have been selected. These regions will serve as the foundation on which to test and evaluate the effectiveness and efficiency of a diverse set of methods and technologies for finding various functional elements in human DNA./ E0 o1 G' o/ f: Y3 d

: d# y8 t, N( [/ R9 [! BFull-length cDNA Project (The Mammalian Gene Collection) [mgc.nci.nih.gov]
3 T+ [  D8 j3 h0 q# Y; i# U0 {The goal of the Mammalian Gene Collection (MGC) project is to identify, sequence and make available to the research community, one representative, full-length (full open reading frame) clone for every human and mouse gene. The MGC website provides information about the confirmed, full ORF clones and cDNA libraries, and describes how to access the resources. The MGC is a trans-National Institutes of Health (NIH) initiative co-led by the National Human Genome Research Institute (NHGRI) and the National Cancer Institute (NCI).
/ q. y0 ~$ S: b2 |
# `! u6 A0 U3 |. AModel Organisms for Biomedical Research [nih.gov]
( V1 f* ?7 _" I* |Provides information and relevant links for trans-NIH model organism initiatives and their related funding opportunities.0 l2 T2 x9 y  z/ f2 i0 t( Q
' m' |( B( w* X0 S* n
Policies
! ^( o  ^1 Z0 XNHGRI Rapid Data Release Policy (January 2003)- d) D$ H2 A" Q

; D, V: U1 Y  ZNIH-DOE Guidelines for Access to Mapping and Sequencing Data and Material Resources (Spring 1998)( Z. Z& F8 m. ^# R

* G4 g& e& ]3 v; g. u9 }5 g8 X1 nFor additional information regarding data release for large-scale sequencing of model organism genomes, see: Guyer, M. Statement on the Rapid Release of Genomic DNA Sequence. Genome Research, 8(5): 413. 1998. [Full Text]1 ^5 F" p2 w& G* q$ d9 z  d) c

7 p9 ?- \/ z) F4 U3 M/ I7 [0 g1 g& ~) b( B: \
" b6 a& w7 y; a5 r8 w9 Z
Top of page, t$ x" o3 _* s& A! M3 T
/ o% Q  N+ X' @1 R- N* f
Functional Analysis Program Funding Opportunities, B% x1 L$ l; y3 q* J
Archival: PA-97-044: Technologies for Genomic Mapping, Sequencing and Analysis [Expired]2 M0 r+ f) ^# i
This announcement solicited investigator-initiated proposals to develop new technologies.
  Z0 T3 W( `. x5 r8 [: Z7 U$ R. @2 s1 b
Centers of Excellence in Genomic Science (CEGS)# |- X- P6 f: X3 I
8 p$ m- a3 G! ~! W% K
Expired Grant Solicitations
: C- N- z0 O4 \6 i5 S# G5 p$ H8 u* S) B0 e7 b" e: c8 Z, j
Top of page
( a- e1 |  h! S+ L' ?2 t2 ?0 A: V" K2 [( Q+ \' @
Functional Analysis Program Staff
) o7 |% l$ i# _Program Directors
  w0 v2 R2 C! ?- JElise Feingold, Ph.D./ L" |% ]& K8 H
E-mail: feingole@exchange.nih.gov3 F0 f, V$ |! e; C& B7 c

- ]3 I4 d5 P8 C5 [7 ~( T) L+ |! cGary Temple, Ph.D.& k( C# t* e2 w6 l) ]
E-mail: gtemple@mail.nih.gov
+ E  v2 I2 f, l0 ~+ @) l) b, A
  }' A- Z) R3 E8 YBettie Graham, Ph.D.8 F) `6 L+ n4 @* B+ ]# _. U) ]7 M0 p
E-mail: grahamb@nhgri.nih.gov) D# n5 _8 ^: m8 [% x

  S- r. G) O5 L2 AProgram Analysts
# g: j. u  L* q& C  N/ v% h1 \7 I& J! d6 a
Cristen Robinson" D. W3 C" L% V9 ~  }1 ]# j
E-mail: robinsoncr@mail.nih.gov' S+ Z3 K2 l  k+ V9 l2 Z  \  A5 h6 G
% h! [( ]+ o8 D- g
Address
! U% o& |4 ]. f2 _1 ANational Human Genome Research Institute
9 _  y* o3 C( G) n1 h  G, g2 dNational Institutes of Health& J' _/ q/ p# J: c" ]6 G
5635 Fishers Lane
3 S0 \9 z) _5 [% N; k" `: A# dSuite 4076, MSC 9305/ q2 B. t$ r: h! l9 J7 t! f
Bethesda, MD 20892-9305: R8 Q, {/ Q" G$ c

( ]- A" Q& g6 w6 [4 iPhone: (301) 496-7531% r- _/ h5 q8 }7 Z$ W5 Q
Fax: (301) 480-2770