1 Supplemental Figure 1 Expression analysis of MPF1-like Withania duplicates The RNAs isolated from leaves, flower buds, sepals, stamens, carpels and siliques.

Slides:

Advertisements

Similar presentations

Predicting Enhancers in Co-Expressed Genes Harshit Maheshwari Prabhat Pandey.

Advertisements

Computational detection of cis-regulatory modules Stein Aerts, Peter Van Loo, Ger Thijs, Yves Moreau and Bart De Moor Katholieke Universiteit Leuven, Belgium.

Finding regulatory modules from local alignment - Department of Computer Science & Helsinki Institute of Information Technology HIIT University of Helsinki.

Regulatory Motifs. Contents Biology of regulatory motifs Experimental discovery Computational discovery PSSM MEME.

Promoter Panel Review. Background related Promoter In genetics, a promoter is a DNA sequence that enables a gene to be transcribed. It may be very long.

Identification of a Novel cis-Regulatory Element Involved in the Heat Shock Response in Caenorhabditis elegans Using Microarray Gene Expression and Computational.

Checking the Required Conditions. Check these 3 boxes.

[Bejerano Fall10/11] 1 Thank you for the midterm feedback! Projects will be assigned shortly.

An analysis of “Alignments anchored on genomic landmarks can aid in the identification of regulatory elements” by Kannan Tharakaraman et al. Sarah Aerni.

Defining the Regulatory Potential of Highly Conserved Vertebrate Non-Exonic Elements Rachel Harte BME230.

Promoter Analysis using Bioinformatics, Putting the Predictions to the Test Amy Creekmore Ansci 490M November 19, 2002.

Finding Regulatory Motifs in DNA Sequences

Promoter structure and gene regulation. Bacterial Promoters Source:

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics.

Supplemental Fig. S1 Ihsan et al., 2015 Supplemental Fig. S1 Sequence analysis of Solanaceous MAGO NASHI genes. ClustalW multiple alignments of nucleotide.

Yuval Hart, Weizmann 2010© 1 Introduction to Matlab & Data Analysis Tutorial 13: That’s all, Folks! Please change directory to directory E:\Matlab (cd.

A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes Angela K. Dean, Stephen E. Harris, Jianhua.

Detecting binding sites for transcription factors by correlating sequence data with expression. Erik Aurell Adam Ameur Jakub Orzechowski Westholm in collaboration.

Figure S1. Genomic PCR of in vitro potato plants transformed with StPTB1 prom (top) and StPTB6 prom (bottom) constructs using nptII-specific primers. Thirty.

Regulation of Gene Expression: An Overview  Transcriptional  Tissue-specific transcription factors  Direct binding of hormones, growth factors, etc.

Multiple Alignment and Phylogenetic Trees Csc 487/687 Computing for Bioinformatics.

COURSE OF BIOINFORMATICS Exam_31/01/2014 A.

ANALYSIS AND VISUALIZATION OF SINGLE COPY ORTHOLOGS IN ARABIDOPSIS, LETTUCE, SUNFLOWER AND OTHER PLANT SPECIES. Alexander Kozik and Richard W. Michelmore.

Figure 2: over-representation of neighbors in the fushi-tarazu region of Drosophila melanogaster. Annotated enhancers are marked grey. The CDS is marked.

The TRANSFAC ® System comprises 7 databases: TRANSFAC ® Professional Suite TRANSFAC ® Professional Transcription factor database TRANSCompel ® Professional.

Comparative Genomics Gene Regulatory Networks (GRNs) Anil Jegga Biomedical Informatics Contact Information: Anil Jegga Biomedical Informatics Room # 232,

T-Coffee tutorial ACGT Retreat 2012 Jean-François Taly, Ionas Erb and Cedrik Magis.

A B IL-4(+) IL-4(-) IL-4(+) IL-4(-) ChIP-Seq (STAT6) Ramos IL-4 (+) P-value Ramos IL-4 (-) P-value BEAS2B IL-4 (+) P-value BEASB IL-4 (-) P-value fold.

Log 2 (expression) H3K4me2 score A SLAMF6 log 2 (expression) Supplementary Fig. 1. H3K4me2 profiles vary significantly between loci of genes expressed.

Tools for Comparative Sequence Analysis Ivan Ovcharenko Lawrence Livermore National Laboratory.

Mucin SCFM MOPS Egg yolk DNA BSA MDTA Supplementary Figure 1. 1 H NMR spectra generated for SCFM media and selected constituents.

-1- Module 3: RNA-Seq Module 3 BAMView Introduction Recently, the use of new sequencing technologies (pyrosequencing, Illumina-Solexa) have produced large.

Arabidopsis Thaliana A Study of Genes and Embryo Development By Garen Polatoglu.

Intro to Probabilistic Models PSSMs Computational Genomics, Lecture 6b Partially based on slides by Metsada Pasmanik-Chor.

Figure S1. RACE mapped transcription starts and polyA signals of Ogre CL5 and Ogre CL5del and putative splice site of Ogre CL5 and Ogre CL5del in Silene.

Pattern Discovery and Recognition for Understanding Genetic Regulation Timothy L. Bailey Institute for Molecular Bioscience University of Queensland.

For this demo you already need the XtAtoh7.maf multiple alignment file from demo (a). Another example.maf file is also available on the ConTra help page.

Supplemental Fig. S1 A B AtMYBS aa AtMYBS

A Very Basic Gibbs Sampler for Motif Detection

Matrix Metalloproteinase 9 Expression is Coordinately Modulated by the KRE-M9 and 12-O-Tetradecanoyl-Phorbol-13-Acetate Responsive Elements Takashi Kobayashi,

Volume 38, Issue 4, Pages (May 2010)

Volume 44, Issue 3, Pages (November 2011)

F.J. Livesey, T. Furukawa, M.A. Steffen, G.M. Church, C.L. Cepko

Suzanne Komili, Natalie G. Farny, Frederick P. Roth, Pamela A. Silver

Volume 44, Issue 1, Pages (October 2011)

Volume 17, Issue 6, Pages (December 2015)

Volume 3, Issue 2, Pages (March 2010)

Volume 93, Issue 7, Pages (June 1998)

Structure of the 5′ Portion of the Human Plakoglobin Gene

Supplemental Figure 3 A B C T-DNA 1 2 RGLG1 2329bp 3 T-DNA 1 2 RGLG2

Mapping Global Histone Acetylation Patterns to Gene Expression

Volume 48, Issue 5, Pages (December 2012)

Quantitative Imaging of Transcription in Living Drosophila Embryos Links Polymerase Activity to Patterning Hernan G. Garcia, Mikhail Tikhonov, Albert.

Volume 128, Issue 6, Pages (March 2007)

Volume 13, Issue 16, Pages (August 2003)

The PHANTASTICA Gene Encodes a MYB Transcription Factor Involved in Growth and Dorsoventrality of Lateral Organs in Antirrhinum Richard Waites, Harinee.

Volume 44, Issue 3, Pages (November 2011)

Volume 30, Issue 4, Pages (May 2008)

Volume 30, Issue 1, Pages (January 2009)

Whorl-Specific Expression of the SUPERMAN Gene of Arabidopsis Is Mediated by cis Elements in the Transcribed Region Toshiro Ito, Hajime Sakai, Elliot.

A Novel Class of MYB Factors Controls Sperm-Cell Formation in Plants

The Arabidopsis Transcription Factor AtTCP15 Regulates Endoreduplication by Modulating Expression of Key Cell-cycle Genes Li Zi-Yu , Li Bin , Dong Ai-Wu.

Volume 8, Issue 7, Pages (July 2015)

Ariel Afek, Itamar Sela, Noa Musa-Lempel, David B. Lukatsky

Volume 7, Issue 2, Pages (August 2010)

Volume 24, Issue 1, Pages 1-10 (January 2014)

Hulusi Cinar, Sunduz Keles, Yishi Jin Current Biology

Volume 2, Issue 2, Pages (March 2009)

Influence of RdDM on DCL4 Transcript Isoform Expression.

Wang Long , Mai Yan-Xia , Zhang Yan-Chun , Luo Qian , Yang Hong-Quan

Presentation transcript:

1 Supplemental Figure 1 Expression analysis of MPF1-like Withania duplicates The RNAs isolated from leaves, flower buds, sepals, stamens, carpels and siliques of Withania somnifera were subjected to real time RT-PCR analysis with gene-specific primers. The columns show the expression of MPF1-like-A of Withania (WSA106; white) and MPF2-like-B of Withania (WSB106; grey)). The values given are relative expression based on three independent experiments normalized with respect to 18S rRNA. Error bars indicate the standard deviation.

2 Supplemental Figure kb -1.7kb -1.1kb-1bp-559 bp Supplemental Figure 2 Mulan (Multiple-sequence local alignment; image of individual MPF2 promoter sequencehttp://mulan.dcode.org Putative cis-acting elements in the promoters were predicted using the plant cis-acting regulatory DNA elements database Transfac ( Concatenated tba.maf files were submitted to MultiTIF in TRANSFAC professional V10 library from plants and matrix similarity optimized for functions was predefined as Eleven out of 80 plant transcription factor families were selected for the creation of TBX5 and NKX 2.5 high quality matrix. The parameters selected for the dynamic overlay of transcription factor binding sites (TFBS) prediction with conservation profile clustering included: 3 kb per layer, picture width of 1200 pixels, one site per 1000 bp and clustering with smooth plot. Finally, the dynamic visualization of TFBS was attained in a graphical format. Scale is also indicated at the base (

3 Supplemental Figure 3 Graphical output shows MPF2-like %age GC contents in a sliding window of 20bp in a range of 0 to 100% Multiple sequence alignment of -2kb promoter region of Solanum, Withania, Tubocapsicum, Physalis and Vassobia was performed with ClustalW program in MacVector software. Shaded area indicates the highest GC content region. Cis-regulatory modules (CRM1, CRM2 and CRM3) are shown on the top of shaded region. A rough scale is also indicated.