Predicting condition specific transcription factors for target gene. - PowerPoint PPT Presentation

Mar 27, 2023 •390 likes •425 views

Predicting condition specific transcription factors for target gene. Kaur Alasoo 19.09.2012 Stress 1 Factor 3 Factor 4 Baseline Stress 2 Factor 1 Factor 2 Factor 1 Factor 2 Target gene ArrayExpress YEASTRACT database

Predicting condition specific transcription factors for target gene. Kaur Alasoo 19.09.2012
Stress 1 Factor 3 Factor 4 Baseline Stress 2 Factor 1 Factor 2 Factor 1 Factor 2 Target gene
�� ArrayExpress YEASTRACT database Disruptome TRAP Differential expression was Analyzed expression Predicted binding affinities of all TF1 Gene 1 Gene 3 Gene 5 Gene 9 calculated in 234 manually data from 269 yeast TFs to the target promoter TF2 TPO1 Gene 2 Gene 4 curated yeast gene ex- TF knock-out strains sequence from Tr anscription TF3 Gene 6 Gene 7 Gene 8 pression data sets from [2]. Factor A ffinity P rediction tool ArrayExpress leading to Known targets of 184 TFs [1]. (TRAP) [3]. 1464 pairwise comparisons. Gene Set Comparisons Analysis 1 2 3 1 Gene 1 Gene 6 TPO1 Differential expression rank TPO1 Gene 9 Gene 2 2 1 2 3 1 TF1 TF2 1 3 Gene 2 TPO1 Gene 6 1 TF1 TF2 TF2 TF2 2 TF10 2 4 Gene 3 Gene 2 Gene 4 2 TF2 TF3 TF1 3 TF4 3 TF3 5 Gene 4 Gene 4 Gene 5 3 TF3 TF1 TF3 4 TF5 4 TF4 p-value p-value 6 Gene 8 Gene 3 Gene 5 5 TF6 5 TF1 Gene 7 7 Gene 6 Gene 8 Rank 6 TF7 6 TF6 Gene 3 Aggregation 8 Gene 9 Gene 7 7 TF3 TF7 7 9 Gene 5 Gene 8 Gene 7 8 8 TF5 TF8 1 TF2 10 Gene 9 Gene 1 Gene 1 9 TF9 9 TF8 score 2 TF1 10 TF10 TF9 10 3 TF3 Ranked list of TFs Ranked list of TFs Ranked list of TFs wild type vs. mutant water vs. ethanol ... Final rank aggregation ��

Recommend

TFClass a classifjcation of transcription factors Jrgen Dnitz, Edgar Wingender T

TFClass a classifjcation of transcription factors Jrgen Dnitz, Edgar Wingender T ranscription factors, the proteins for regulation of transcription Transcription factors are proteins that regulate transcription by binding to specifjc

419 views • 18 slides

Theoretical Biology 2016 Transcription factors bind DNA to block or enhance transcription

Chapter 7 Gene regulation Theoretical Biology 2016 Transcription factors bind DNA to block or enhance transcription From Campbell DNA makes RNA makes protein Golding et al. Cell 2005 d M d P d t = lM P d t = c dM and mRNA

458 views • 23 slides

Section 12.0 Transcription Factors, Binding Sites, and the Challenge of Finding Novel Problems

Section 12.0 Transcription Factors, Binding Sites, and the Challenge of Finding Novel Problems in Bioinformatics ? Wyeth Wasserman www.cisreg.ca Overview TFBS Prediction with Motif Models Improving Specificity of Predictions

614 views • 57 slides

Understanding the mode of action of the symbiosis-specific NF-YA1 transcription factor in Medicago

Understanding the mode of action of the symbiosis-specific NF-YA1 transcription factor in Medicago truncatula Carolina Rpodas Laboratoire des Interactions Plantes-Microorganismes INRA - Toulouse Paris, 13 th -16 th February 2017 AgreenSkills

234 views • 5 slides

Identification Polymorphism of Pituitary-Specific Positive Transcription Factor 1(Pit1) Gene in

Identification Polymorphism of Pituitary-Specific Positive Transcription Factor 1(Pit1) Gene in Indonesian Swamp Buffalo (Bubalus bubalis) and Holstein-Friesian Cows R. Misrianti a , C. Sumantri a , and A. Farajallah b a) Faculty of Animal

477 views • 24 slides

Lessons learned from transcription factor co-association analysis The enhancer-promoter

Lessons learned from transcription factor co-association analysis The enhancer-promoter interaction model encoded by the transcription factors AP-1 and NF-Y Workshop on Bioinformatics of Gene Regulation Gttingen, March 7-9 2018 Institute of

251 views • 13 slides

Support for this research: Factors Predicting Sustained OSEP: TA Center on PBIS (H326S03002)

Support for this research: Factors Predicting Sustained OSEP: TA Center on PBIS (H326S03002) Implementation of UBC Hampton Endowment Fund (J07-0038) School-based Behaviour Social Sciences and Humanities Council Support Interventions

190 views • 6 slides

Using Network Component Analysis to Dissect Regulatory Networks Mediated by Transcription Factors

Using Network Component Analysis to Dissect Regulatory Networks Mediated by Transcription Factors in Yeast PLoS Computa,onal Biology, Ye et al. 02-715 Advanced Topics in Computa,onal

329 views • 18 slides

BRAF Mutated mCRC: Specific Considerations for Treatment Dustin Deming, MD McArdle Laboratory

BRAF Mutated mCRC: Specific Considerations for Treatment Dustin Deming, MD McArdle Laboratory of Cancer Research Carbone Cancer Center University of Wisconsin EGFR PI3K RAS AKT P BRAF P BRAF P MEK MAPK P N u Transcription factors

539 views • 20 slides

Case study: Finding a new DNA binding domain Stockholm, November 8 2018 Jakub Orzechowski

Case study: Finding a new DNA binding domain Stockholm, November 8 2018 Jakub Orzechowski Westholm Long-term bioinformatics support NBIS, SciLifeLab, Stockholm University Transcription factors Transcription factors typically consist of

618 views • 40 slides

Identification of associated transcription factors in promoters and their related enhancer regions

Identification of associated transcription factors in promoters and their related enhancer regions Cornelia Meckbach Institute of Bioinformatics March 8, 2018 Cornelia Meckbach (Inst. of Bioinf.) Associated TFs in enhancer and promoters March

417 views • 20 slides

Genome-wide Survey of Mixed MicroRNA / Transcription Factor Feed-Forward Regulatory Circuits in

Genome-wide Survey of Mixed MicroRNA / Transcription Factor Feed-Forward Regulatory Circuits in Human Davide Cor University of Torino and INFN cora@to.infn.it Transcription Factors and miRNAs Regulation of gene expression mainly

502 views • 22 slides

Introduction Collection of proteins called transcription factors mediate binding of RNA

22/07/54 Oral Pre se ntatio n CRDC 5 The 5 th Tropical and Sub-tropical Crops The 5th Tropical and Sub tropical Crops Research Symposium (CRDC5) Research Symposium (CRDC5) Responses of Transcription Factor to Oxidative Stress in Saccharomyces

486 views • 17 slides

14.54 International Trade Lecture 12: Specific Factors Model (II) 14.54 Week 7 Fall 2016 14.54

14.54 International Trade Lecture 12: Specific Factors Model (II) 14.54 Week 7 Fall 2016 14.54 (Week 7) Specific Factors Model (II) Fall 2016 1 / 24 Todays Plan Refresher on Specific Factor Model 1 Effects of Changes in Factor

368 views • 24 slides

Specific Learning Disabilities Webinar 4: Exclusionary Factors and English Learners February

Specific Learning Disabilities Webinar 4: Exclusionary Factors and English Learners February 2017 Objectives Increase your confidence in: l Considering Exclusionary Factors during an evaluation for SLD l Using formal assessment results and

544 views • 26 slides

Factors predicting connection to nature Misha Voloaca Supervisor: Veronika Huta University of

Factors predicting connection to nature Misha Voloaca Supervisor: Veronika Huta University of Ottawa Overview Connection to nature? Trends Qualitative study highly connected Quantitative study general public What is

354 views • 21 slides

14.54 International Trade Lecture 11: Specific Factors Model 14.54 Week 6 Fall 2016

14.54 International Trade Lecture 11: Specific Factors Model 14.54 Week 6 Fall 2016 14.54 (Week 6) Specific Factors Model Fall 2016 1 / 22 Todays Plan 1 Setup Autarky and Trade Equilibrium 2 Impact of Trade 3 Graphs on

363 views • 22 slides

and a model for robust community participation Wyeth W. Wasserman 30 November 2010

The wiki-based Transcription Factor Encyclopedia and a model for robust community participation Wyeth W. Wasserman 30 November 2010 http://www.cisreg.ca/tfe Transcription Factors 101 Diverse set of proteins sharing common functional role

458 views • 29 slides

DNA Binding Proteins CSE 527 Autumn 2007 A variety of DNA binding proteins (transcription

DNA Binding Proteins CSE 527 Autumn 2007 A variety of DNA binding proteins (transcription factors; a significant fraction, Lectures 8-9 (& part of 10) perhaps 5-10%, of all human proteins) Motifs: Representation & Discovery

625 views • 16 slides

USING RADON AS A SURROGATE FOR VOCS TO DETERMINE BUILDING- SPECIFIC ATTENUATION FACTORS IN VAPOR

USING RADON AS A SURROGATE FOR VOCS TO DETERMINE BUILDING- SPECIFIC ATTENUATION FACTORS IN VAPOR INTRUSION ASSESSMENTS AEHS CONFERENCE SESSION #4 Gannett Fleming, Inc October 16, 2018 Before We Start Who is Here? State or Federal

977 views • 39 slides

What are Right-of-Way Certifications? What makes a ROW Certification a Condition 1? What makes

What are Right-of-Way Certifications? What makes a ROW Certification a Condition 1? What makes a ROW Certification a Condition 2? What makes a ROW Certification a Condition 3? The specific requirements for this action are found at 23 CFR

869 views • 20 slides

Transcription: Pausing and Backtracking: Error Correction Mamata Sahoo and Stefan Klumpp Theory

Transcription: Pausing and Backtracking: Error Correction Mamata Sahoo and Stefan Klumpp Theory and Bio-systems group, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany Transcription Transcription is the efficient regulatory

386 views • 16 slides

Unsupervised Piano Music Transcription Taylor Berg-Kirkpatrick Jacob Andreas and Dan Klein

Unsupervised Piano Music Transcription Taylor Berg-Kirkpatrick Jacob Andreas and Dan Klein CMU UC Berkeley Piano Music Transcription note time Supervised Transcription Supervised Transcription w Model

891 views • 56 slides

ECON2915 Economic Growth Lecture 10 : Specific Factors. Andreas Moxnes University of Oslo Fall

ECON2915 Economic Growth Lecture 10 : Specific Factors. Andreas Moxnes University of Oslo Fall 2016 1 / 34 Introduction Recall, in Ricardian model: Two products (e.g. rice and cocoa) and one input (labor). Trade occurs because of relative

605 views • 37 slides