Prediction of transcription factor binding to DNA using rule induction methods

Sep 11, 2012

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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

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Prediction of transcription factor binding to DNA using rule induction methods

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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)

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DNA Transcription

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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.

731 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.

837 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?

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Rule Induction

Rule Induction.

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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.

424 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)

287 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

640 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

427 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?

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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.

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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).

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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

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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.

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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

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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.

494 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).

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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?

548 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

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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!.

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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.

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