Prediction of transcription factor binding to DNA using rule induction methods

Sep 11, 2012

250 likes | 445 Views

Background. Pax transcription factors are found in all animals. They are important for developmental processes (e.g. eye formation and neural development) and may also be involved in cancerogenesis. In humans, Pax mutations can result in e.g. Waardenburg's syndrome (an inherited disorder often cha

Share Presentation

Embed Code

Link

emory

Download Presentation

Prediction of transcription factor binding to DNA using rule induction methods

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

Sequence features of DNA binding sites reveal structural class of associated transcription factor

Sequence features of DNA binding sites reveal structural class of associated transcription factor Narlikar L and Hartemink AJ. Bioinformatics. 2006 Jan 15;22(2):157-63. Carol Sniegoski The Central Dogma of Molecular Biology Double-stranded chain of nucleotide bases (A-T, C-G)

1.35k views • 44 slides

DNA Transcription

566 views • 38 slides

Identification of Transcription Factor Binding Sites

Identification of Transcription Factor Binding Sites. Presenting: Mira & Tali. AGCCA AGCCA AGCCA AGCCA AGCCA. Goal. Regulatory regions. Motif – Binding site???. AGCCA. Why Bother?. UNDERSTAND. Gene expression regulation. Co-regulation. Difficulties.

748 views • 46 slides

DNA Transcription

DNA Transcription . Chapter 12. DNA Transcription:. The Central Dogma of Genetics Promoters, Transcription Factor, and RNA Polymerases Steps of Transcription Post-Transcriptional Modifications, of RNA. Central Dogma of Molecular Biology.

873 views • 23 slides

Searching for transcription factor binding sites with TRANSFAC

Searching for transcription factor binding sites with TRANSFAC. George Bell, Ph.D. Bioinformatics and Research Computing Hot Topics – October 2009. Outline. What is known about your favorite TFs? In what regulatory DNA should we search?

498 views • 21 slides

Rule Induction

Rule Induction.

531 views • 31 slides

Engineering Transcription Factors with Novel DNA-Binding Specificity using Comparative Genomics

Engineering Transcription Factors with Novel DNA-Binding Specificity using Comparative Genomics. Tasha A. Desai, Dmitry A. Rodionov , Mikhail S. Gelfand , Eric J. Alm , and Christopher V. Rao. Alvin Chen 20.385 April 14, 2010. Comparative Genomics.

438 views • 24 slides

Detection of Transcription Factor Binding Sites

Detection of Transcription Factor Binding Sites. Michael Morra CSE 4939W. Project Recap. Implement a method used to accurately and precisely discover the locations of transcription factor binding sites within a DNA sequence. 4 species (Human, Mouse, Fruit Fly & Yeast)

296 views • 12 slides

Finding Transcription Factor Binding Sites

Finding Transcription Factor Binding Sites. BNFO 602/691 Biological Sequence Analysis Mark Reimers, VIPBG. Why TFBS?. Protein transcription factors were among the first gene regulators identified Many TFBS have distinct sequences, which were suitable for bioinformatics analysis

662 views • 30 slides

DNA-binding Residues and Binding Mode Prediction with Binding-Mechanism Concerned Models

DNA-binding Residues and Binding Mode Prediction with Binding-Mechanism Concerned Models. Yu- Feng Huang 1 , Chun-Chin Huang 2 , Yu-Cheng Liu 3 , Yen-Jen Oyang 1,4,5 , Chien -Kang Huang 2 * 1 Department of Computer Science and Information Engineering

445 views • 25 slides

Finding Transcription Factor Binding Sites

Finding Transcription Factor Binding Sites. BNFO 602/691 Biological Sequence Analysis Mark Reimers, VIPBG. Questions . If know motif (or sequence binding preferences) can you identify likely active TFBS? If you have a TF, can you find its motif and binding sites?

393 views • 21 slides

Bio277 Lab 3: Finding Transcription Factor Binding Motifs

Bio277 Lab 3: Finding Transcription Factor Binding Motifs. Adapted from a Lab Written by Prof Terry Speed Jess Mar Department of Biostatistics Quackenbush Lab DFCI jmar@hsph.harvard.edu. Outline. Analyze cell cycle gene expression data.

281 views • 15 slides

Location Analysis of Transcription Factor Binding

Location Analysis of Transcription Factor Binding. Tommy Computational Biology Seminar Nov. 2005. Background. Immuno Precipitation ChIP - Chromatin Immuno Precipitation Microarray evolution (from promoter arrays to tiling arrays) ChIP-chip (ChIP followed by microarray hybridization).

736 views • 48 slides

DNA binding domains and activation domains of transcription factors

DNA binding domains and activation domains of transcription factors. A survey of DNA binding domains. Zn -containing domains 6 Cys and 2 Zn: Gal4 Zn fingers Many eukaryotic transcription factors Basic-leucine zipper proteins (hetero)Dimers, eukaryotic activators Helix-turn-helix

446 views • 12 slides

Last time … * Constraint on transcription factor binding sites

Last time … * Constraint on transcription factor binding sites Sites with the most ‘ information content ’ generally evolve slowest * Stabilizing selection via binding site turnover * Gain and loss of orthologous binding sites can correlate with gain and loss of target genes.

357 views • 18 slides

Transcription factor binding sites and gene regulatory network

Transcription factor binding sites and gene regulatory network. Victor Jin Department of Biomedical Informatics The Ohio State University. Transcription in higher eukaryotes. Gene Expression Chromatin structure Initiation of transcription Processing of the transcript

550 views • 25 slides

Identification of Transcription Factor Binding Sites

Identification of Transcription Factor Binding Sites. Lior Harpaz Ofer Shany 09/05/2004. Goal - find TFBS !. input. output. Importance. TF regulate gene expression. Identification of TF can teach us: Mapping of regulatory pathways Potential functions of genes. Experimental Methods.

508 views • 31 slides

Transcription factor binding motifs (part II)

Transcription factor binding motifs (part II). 10/22/07. Information from negative control. Motivation: combine information from TF binding and non-binding sequences to identify discriminative information. Methods: REDUCE (Bussmaker et al. 2001) Motif Regressor (Conlon et al. 2003).

580 views • 45 slides

Transcription factor binding motifs (part I)

Transcription factor binding motifs (part I). 10/17/07. Steps of gene transcription. Pol II. TFIID. activator. TATA. The term “transcription factor” (TF) usually means an activator or repressor. Understand Regulation. Which TFs are involved in the regulation?

567 views • 40 slides

Detection of Transcription Factor Binding Sites

Detection of Transcription Factor Binding Sites. Michael Morra CSE 4939W. Background. DNA is comprised of a combination of 4 chemical bases Adenine – A Thymine – T Guanine – G Cytosine - C. Background (Continued). Each individual organism has a unique DNA sequence

326 views • 16 slides

Location analysis of transcription factor binding sites

Location analysis of transcription factor binding sites. Guy Naamati Andrei Grodzovky. A brief history. What about today?. Two weeks ago Masha and Michal told us about gene expression and gene clusters. Last week, Lior and Ofer told us about tfbs, and how to identify them. Today!.

830 views • 65 slides

Using Mixed Length Training Sequences in Transcription Factor Binding Site Detection Tools

Using Mixed Length Training Sequences in Transcription Factor Binding Site Detection Tools. Nathan Snyder Carnegie Mellon University. BioGrid REU 2009 University of Connecticut. Transcription Factors. Transcription factors regulate DNA transcription.

255 views • 14 slides

More Related