TF candidate selection pipeline.

Slides:

Advertisements

Similar presentations

Putting TAIR to work for you hands-on workshop for beginning and advanced users

Advertisements

LS-SNP: Large-scale annotation of coding non- synonymous SNPs based on multiple information sources -Bioinformatics April 2005.

Protein Structure Database Introduction Database of Comparative Protein Structure Models ModBase 生資所 g 詹濠先.

Reconstructing Transcription Network in S.cerevisiae WANG Chao Oct. 4, 2004.

Domain Assignment to Transcription Factors 416 Proteins with at least one SCOP DBD assignment 416 Proteins with at least one SCOP DBD assignment PFAM assignments.

BACKGROUND E. coli is a free living, gram negative bacterium which colonizes the lower gut of animals. Since it is a model organism, a lot of experimental.

1 SRI International Bioinformatics Advanced PGDB Editing: Regulation GO Terms Ingrid M. Keseler Bioinformatics Research Group SRI International

BASys: A Web Server for Automated Bacterial Genome Annotation Gary Van Domselaar †, Paul Stothard, Savita Shrivastava, Joseph A. Cruz, AnChi Guo, Xiaoli.

Anis Karimpour-Fard ‡, Ryan T. Gill †,

Building WormBase database(s). SAB 2008 Wellcome Trust Sanger Insitute Cold Spring Harbor Laboratory California Institute of Technology ● RNAi ● Microarray.

Genome annotation and search for homologs. Genome of the week Discuss the diversity and features of selected microbial genomes. Link to the paper describing.

No reference available

Module 5: Future 1 Canadian Bioinformatics Workshops

Detecting Protein Function and Protein-Protein Interactions from Genome Sequences TuyetLinh Nguyen.

Welcome to the Protein Database Tutorial. This tutorial will describe how to navigate the section of Gramene that provides collective information on proteins.

BUSINESS SENSITIVE 1 SAAW - Sequence Annotation and Analysis Workshop Boyu Yang and Gene Godbold Battelle Memorial Institute, Charlottesville Operations.

A New Interface to GeneKeyDB Methods for analyzing relationships among proteins based on shared motifs Chris Symons & Xinxia Peng.

Introduction to Biomedical Engineering Tutor: Susana Vinga, INESC-ID/FCM-UNL Master in Biomedical Engineering, IST/FML 2011/2012 Ana de Aguiar nº 72727;

Bacteriophage Gene Functions

PINALOG Protein Interaction Network Alignment and its implication in function prediction and complex detection Hang Phan Prof. Michael J.E. Sternberg.

The Integrated Microbial Genome (IMG) systems

Sungkyunkwan University, School of Medicine.

Control of Gene Expression

Sequence based searches:

Interrogation of cross talk between proteins and gene regulatory networks in breast cancer Chambers, Teressa Lee Hiren Karathia Sridhar Hannenhalli.

Genome-wide CRISPR screen to determine

Saccharomyces Genome Database (SGD)

Functional Annotation Final Results

Functional Annotation of the Horse Genome

Predicting Active Site Residue Annotations in the Pfam Database

The Functional Impact of Alternative Splicing in Cancer

Advanced PGDB Editing: Regulation GO Terms

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Proposed schemes for OXT biosynthesis using the proteins encoded by the oxsA and oxsB production genes, which are annotated as an HD domain phosphohydrolase.

Adding Specificity to Artificial Transcription Activators

SIFGD: Setaria italica Functional Genomics Database

Alignment of H-NS, H-NS2, and StpA amino acid sequences.

The Functional Impact of Alternative Splicing in Cancer

Predicted location and functional classification of differentially expressed transcripts. Predicted location and functional classification of differentially.

Transcriptomic and proteomic data sets available in the Listeriomics database. Transcriptomic and proteomic data sets available in the Listeriomics database.

Volume 20, Issue 11, Pages (September 2017)

Meta-analysis of the Listeriomics transcriptomic data sets.

Correlation of mouse gene expression with bacterial gene expression.

ChIP-seq Robert J. Trumbly

Parallel evolution of coding sequences above neutral expectation.

Protein information in the Human Protein Atlas.

The Human Transcription Factors

Characterization of differentially expressed proteins based on their COG classification. Characterization of differentially expressed proteins based on.

Overview Domains and conclusion Introduction Biological network data

Tissue Western analysis of purified monospecific antibodies.

Wiley Interdiscip Rev Dev Biol May;7(3):e314

Putative targets of miRNAs directly induced by p53 with down-regulated mRNA- and de novo protein synthesis or reduced de novo protein synthesis only. Putative.

Example usage of mockrobiota MC resource for marker gene and metagenome sequencing pipelines. Example usage of mockrobiota MC resource for marker gene.

Functional prediction of unknown proteins in S. pneumoniae.

Diagram of experimental design.

Pathway analysis of genes upregulated after RSV infection.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Proportion of 16S rRNA gene sequences in each category of phylogenetic novelty relative to cultures for each environment, by amplicons, metagenomes (without.

Fraser Fraser 2000 Metzker 2010 Metzker 2010.

Alignment of putative chicken HB-EGF to mammalian HB-EGF proteins and the domains of HB-EGF. Alignment of putative chicken HB-EGF to mammalian HB-EGF proteins.

Characterization of differentially expressed genes based on their COG classification. Characterization of differentially expressed genes based on their.

FoxB protein binds directly to the cis-regulatory element of the Bra gene. FoxB protein binds directly to the cis-regulatory element of the Bra gene. (A)

Exploring a Putative Gene

Sequence variation of 16S rRNA gene primer-binding sites.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Venn diagram of the distribution of protein CDSs inferred from the genomes of A. hydrophila ATCC 7966T, E1, and E2. Venn diagram of the distribution of.

Fig. 1. Schematic description of whole-exome or targeted next-generation sequencing analyses. Schematic description of whole-exome or targeted next-generation.

Relative abundance and expression of the 10 most abundant MAGs in the bioreactor at day 96. Relative abundance and expression of the 10 most abundant MAGs.

Diagrammatic view of the locations of genes encoding classical HLA class I (HLA-A, -B, -C, -E, -F, and -G) and class II (DR, DQ, DP, and DM) molecules.

Presentation transcript:

TF candidate selection pipeline. TF candidate selection pipeline. Genes encoding proteins with a putative DNA binding domain were annotated using sequence databases PFAM (37) and PSI-BLAST (38), structural predictions (26), and protein functions from COG (39). These annotations were stored in the Systems Biology Experiment and Analysis Management System (SBEAMS) database (36), resulting in 130 putative TFs. Transcriptome analysis across 1,495 experimental conditions (43) and GRN network inference models (7, 15) were then used to generate predictions regarding TF functions. Details of GRN predictions and criteria for selection of the final collection of 27 TFs are given in Table S1 in the supplemental material. DBD, DNA binding domain. Cynthia L. Darnell et al. mSystems 2017; doi:10.1128/mSystems.00032-17