Structural properties of 2954 OsMADS1-bound sequences in three data sets (intergenic, gene body, and A-tract). Structural properties of 2954 OsMADS1-bound.

Slides:

Advertisements

Similar presentations

PREDetector : Prokaryotic Regulatory Element Detector Samuel Hiard 1, Sébastien Rigali 2, Séverine Colson 2, Raphaël Marée 1 and Louis Wehenkel 1 1 Bioinformatics.

Advertisements

Run restriction digestion: TA's will take the pictures for you.

Figure S1_Yao Qin et al. Figure S1 Occurrence and distribution of trihelix family in different plant species. Red branches in the cladogram indicate that.

발표자 석사 2 년 김태형 Vol. 11, Issue 3, , March 2001 Comparative DNA Sequence Analysis of Mouse and Human Protocadherin Gene Clusters 인간과 마우스의 PCDH 유전자.

DNA-Protein Interactions & Complexes. Prokaryotic promoter Consensus sequence is not present in majority of prokaryotic promoters. Sequence motifs.

1 In Silico Identification of Promoters in Prokaryotic Genomes Manju Bansal Molecular Biophysics Unit Indian Institute of Science Bangalore

Phylogenetic analysis of CADs and oxidoreductases involved in specialized metabolism (ORSMs). Phylogenetic analysis of CADs and oxidoreductases involved.

binding sites 58 of the 473 unambiguously assigned phosphorylation sites are predicted by Scansite to be sites for binding. 50 of these correspond.

Sequence alignment of C-terminal phosphorylated plant aquaporins

Volume 10, Issue 7, Pages (July 2017)

Dual-Luciferase Activation Assay with Potential Targets of ZmbZIP22.

Volume 94, Issue 12, Pages (June 2008)

cpDNAs with large deletions accumulate in cptk1 mutants.

Identification of chromosomal regions that exhibit evidence of selection. Identification of chromosomal regions that exhibit evidence of selection. Allele.

The 130-bp key region of the promoter of TsVP1 is a direct binding target of TsNAC1. The 130-bp key region of the promoter of TsVP1 is a direct binding.

Diagrammatic representation of the proposed first three levels of amylopectin (Ap) structure (adapted from Gallant et al., 1997). Diagrammatic representation.

AGL15 Interacts in a Sequence-Specific Manner with a Noncanonical CArG Motif Present in the Regulatory Region of AtGA2ox6.(A) Enrichment of the AtGA2ox6.

Volume 83, Issue 5, Pages (November 2002)

The Antisense Transcriptomes of Human Cells

Evidence for Widespread Reticulate Evolution within Human Duplicons

Molecular cloning of pms916 salt hypersensitive T-DNA mutant.

Mapping Global Histone Acetylation Patterns to Gene Expression

MSI and cutin and suberin composition analyses in reticulated and in-between smooth regions of fruit skin tissues. MSI and cutin and suberin composition.

Presented by, Jeremy Logue.

Example outputs from the updated Arabidopsis Interactions Viewer.

Presence of motifs correlated with decreased expression of downstream genes. Presence of motifs correlated with decreased expression of downstream genes.

Novel p53 target genes identified by RNA-Seq, pSILAC and ChIP-Seq.

N-terminal extension of a gene using peptides mapping upstream to an annotated start site. N-terminal extension of a gene using peptides mapping upstream.

Volume 128, Issue 6, Pages (March 2007)

MC and JOINTLESS form a heterodimer with DNA-binding ability.

Expression analysis of MC and JOINTLESS

Validation of ChIP-seq reads.

Genome-wide binding sites of OsMADS1 and the distribution of binding sites in different regions of annotated genes. Genome-wide binding sites of OsMADS1.

Quantitative RT-PCR results of relative gene expression normalized to wild-type (WT) expression levels for the LjMYB14 transgene (A) and genes specific.

Network analysis of some transcription factors and chromatin regulators that are directly and positively regulated by OsMADS1. Network analysis of some.

Nora Pierstorff Dept. of Genetics University of Cologne

Structural Flexibility of CaV1. 2 and CaV2

Mapping of the FD binding site in the AP1 promoter.

RNA-seq results at the SAM

Identification of FD targets by pSUC2::GFP:FD ChIP-seq in Col-0 and ft-10 tsf-1 and pFD::GFP:FD ChIP-seq in fd-2. Identification of FD targets by pSUC2::GFP:FD.

Enrichment analysis of differentially methylated CpGs.

Expression and Histone H4 Acetylation Levels of MAPK6 and WRKY53 in the HDT701 OX and RNAi Plants after M. oryzae Inoculation. Expression and Histone H4.

Effects of single and combined stresses on plant development and productivity. Effects of single and combined stresses on plant development and productivity.

Presented by, Jeremy Logue.

Occurrence of fur−-only genes and expected sensitivity to Fur.

Sequence dependence of Met4 recruitment.

Summary of differentially expressed genes.

Phenotyping of three hvcen mutants (mat-c. 907, mat-c. 94, mat-c

Inactivation of BOP1, BOP2, TGA1, and TGA4 corrects pny pnf meristem arrest. Inactivation of BOP1, BOP2, TGA1, and TGA4 corrects pny pnf meristem arrest.

Mitochondrial enzymatic activities and root tip respiration in wild type (WT) and mab1-1. Mitochondrial enzymatic activities and root tip respiration in.

Two cycad AOX genes, CrAOX1 and CrAOX2, showing different expression patterns in thermogenic male cones. Two cycad AOX genes, CrAOX1 and CrAOX2, showing.

Numerical analysis of cell morphology of tapetal cells in wild type.

ChIP-seq for H3K4me and H3K27ac assigns potential enhancers to transcripts under control of HoxA9. ChIP-seq for H3K4me and H3K27ac assigns potential enhancers.

High Sensitivity Profiling of Chromatin Structure by MNase-SSP

Structural Variations of the Kala4 Promoters in 21 Black Rice Varieties.The Kala4 promoters of 21 black rice varieties were classified into three types.

Structure of Wt1 genomic regions in human and zebrafish.

Multiplexed Mutagenesis Using the Csy4 System in Tomato Protoplasts.

Bicuculline-sensitive current sharpened the frequency response.

Fig. 5 Stability of the Q parameter.

OsSHI1 Binds Directly to the Promoter Regions of OsTB1 and OsDEP1.

Identification of a ufo1 Candidate Gene from the Mapping Region.

Predicted Amino Acid Sequence of the Tomato Cf-4 Protein (Thomas et al

Next-Generation Sequencing of Duplication CNVs Reveals that Most Are Tandem and Some Create Fusion Genes at Breakpoints Scott Newman, Karen E. Hermetz,

Analysis of A-to-I RNA edits found in transcriptome-wide RNA-seq

CCA1 Binds the Promoter of GI in Vitro and in Vivo.

Fig. 3 Effects of plant species identity, plant traits, and soil properties on plant-soil feedbacks. Effects of plant species identity, plant traits, and.

S. moellendorffii BBI3 Is Predicted to Be a BBI Based on Sequence Similarity at the Inhibitory Motifs and Shared Primary Protein Architecture. S. moellendorffii.

AtSPO11-1–Dependent sRNAs Show Enrichment at Meiotic CO-Associated DNA Motifs. AtSPO11-1–Dependent sRNAs Show Enrichment at Meiotic CO-Associated DNA Motifs.

Integrated analysis of gene expression and copy number alterations.

Comparison of Different Systems for Expressing Multiple gRNAs.

Presentation transcript:

Structural properties of 2954 OsMADS1-bound sequences in three data sets (intergenic, gene body, and A-tract). Structural properties of 2954 OsMADS1-bound sequences in three data sets (intergenic, gene body, and A-tract). Sequences were aligned by positioning the CArG or A-tract motif at 0. Structural properties for sequences spanning 250 bp upstream and 250 downstream were calculated. Profiles for shuffled sequences for each data set are presented as controls in the same color as the respective OsMADS1-bound data set, but with a dashed line. A, The frequency of occurrence of A-tracts in all data sets shown only for the −100 to +100 region for clarity. B, DNA double helix stability was represented by AFE in kcal/mol. Smaller values indicate greater stability. C, Bendability or flexibility was measured by predicting DNaseI sensitivity. Smaller values suggest less bendability. D, Distribution of curvature around the motif was calculated by using BMHT dinucleotide parameters for all three data sets and their randomized controls. Smaller values indicate higher curvature. Imtiyaz Khanday et al. Plant Physiol. 2016;172:372-388 ©2016 by American Society of Plant Biologists