Agilent GeneSpring GX 10: Beyond. Pam Tangvoranuntakul Product Manager, GeneSpring October 1, 2008
|
|
|
- Kristopher Parsons
- 6 years ago
- Views:
Transcription
1 Agilent GeneSpring GX 10: Gene Expression and Beyond Pam Tangvoranuntakul Product Manager, GeneSpring October 1, 2008
2 GeneSpring GX 10 in the News
3 Our Goals for GeneSpring GX 10 Goal 1: Bring back GeneSpring GX features most requested by users Update annotations directly from NCBI Normalization options: control genes, scaling, baseline transformation to multiple control groups Ability to plot raw intensity values And many more Goal 2: Improve features in GeneSpring GX 9 Automate GX 7 to GX 9 Migration tool Hierarchical Clustering: improve visualization and navigation, color branches by parameters, mouse-over to show correlation coefficient Flexible GO annotation formats And many more Goal 3: Add analysis tools for new applications Analysis of mirna expression using Agilent mirna microarray data Analysis of alternative splicing using Affymetrix Exon Array data Analysis of ABI real-time PCR data Network analysis using interactions from Pathway Architect knowledge base or interactions extracted from text using NLP
4 New Applications and Analyses: mirna, alternative splicing, pathway analysis, and real-time PCR alternative splicing gene expression real-time PCR mirna pathway analysis
5 Agilent mirna Data Analysis in GeneSpring GX 10 MicroRNAs (mirnas) may regulate up to 90% of the human transcriptome mirnas regulate expression through translation repression and mrna degradation Recently, evidence of mirna inducing i gene expression has been presented Changes in mirna expression can lead to changes in gene expression that mediate the underlying mechanism of a biological process or disease
6 Agilent mirna Data Analysis in GeneSpring GX 10 Support for Agilent mirna data Download mirna technologies in GeneSpring GX Full text files from FE automatically recognized Guided Workflow for Agilent mirna array data Normalization QC on Samples using Agilent Feature Extraction (FE) QC metrics QC on mirs using Agilent FE probe QC metric Statistical Analysis Fold change analysis GO Analysis on significant ifi mir targetst Pathway Analysis on mir targets
7 Biological Contextualization of mirna Data What are the targets of these differentially expressed mirs? Is there an enrichment of these targets in any GO term? Is there an enrichment of these targets in any pathways? Biological Knowledge: Intracellular trafficking and cell motility are affected and may mediate disease process under study Biological Knowledge: TGF-beta signaling and cell-cycle regulation pathways are affected and may mediate disease process under study
8 View mir Target Expression Values Gene targets of differentially expressed mirs can be translated into a corresponding gene expression experiment to view their expression levels
9 Alternative Splicing Analysis Approximately 75 percent of human mrnas undergo alternative splicing Splice variants can produce proteins with distinct and sometimes even antagonistic functions A number of genetic mutations associated with human disease map to changes in splicing signals or sequences that regulate splicing Thus, measuring changes in splicing patterns is integral to understanding the disease mechanism or biological process under study
10 Alternative Splicing Analysis in GeneSpring GX 10 Support for Affymetrix GeneChip Exon Arrays Perform both gene-level (gene expression) and exon-level (alternative splicing) analysis Summarize Core, Extended, or Full probe sets using RMA, PLIER, or IterPLIER QC on samples and QC on exons using Affymetrix QC metrics Identify alternative splicing activities using the multivariate splicing ANOVA
11 Identification and Visualization of Differentially Spliced Transcripts Transcripts with significantly different splicing events are identified using a multivariate splicing ANOVA Significant transcripts can be filtered on splicing index value ( fold change analysis at the exon level) Each transcript can be plotted using: Variance Plot- profile represents average intensity values or gene normalized intensity values for each condition across probes of the chosen transcript (Red: Normal, Blue: Tumor) Probesets on x-axis are ordered according to their chromosomal location Profile Plot- profile represents intensity values for each probeset in each condition
12 Real Time RT-PCR Data Analysis in GeneSpring GX 10 Support for ABI 7900 real-time PCR platform SDS 2.1, 2.2, and 2.3 RQ file formats supported RQ Manager 1.2 file format supported All analysis tools available to apply to data (statistical tests, fold change analysis, clustering etc) Results of real-time RT-PCR data can be directly compared to microarray gene expression data in GeneSpring GX 10 Differentially expressed genes validated by realtime PCR experiment Differentially expressed genes identified in microarray experiment
13 Improved Data Translation Tool Expression data and list associated values for list also imported to experiment you are translating to Translate Affymetrix list to Agilent 1 color experiment Homology table displayed Entity list associated values and raw or normalized intensity values from original experiment can be plotted in target experiment using Plot Entity List Associated Value tool
14 Plot Entities by Entity List Values Plot Entities from up to two Entity Lists in Scatter Plot, Profile Plot, and Histogram All Entity List associated values and raw or normalized intensity values can be plotted for those Entities If two Entity Lists are used, the union of those lists are plotted Color entities by any Entity List values Entity List translated from other experiments can also be plotted and intensity values are those from the other experiment
15 Compare Results From Maximum of Three Experiments Using Venn Diagram Project up to three Entity Lists from different experiments (of different platforms or species) to the Venn Diagram Translation between platforms and species is performed automatically Allows comparison of results between different experiments
16 Pathway Analysis in GeneSpring GX 10 Find Significant Pathway analysis has been added to each Guided Workflow Full integration of tools in PathwayArchitect Import and view Biopax pathways and perform Find Similar Pathways analysis as in GX 9 Create interaction network using entities of interest Direct interaction network, expand network, shortest path network, network regulators, and network targets Create relevance interaction network using entities of interest Generate an interaction network with an associated (high) confidence index Is the number of interactions between my entities of interest greater than what would be expected by chance? Overlay expression data onto pathways Use Natural Language Processing (NLP) algorithm to mine full text files and Medline abstracts in PubMed to create new interactions and pathways
17 Superimpose Expression Data onto Pathways
18 Pathway Analysis in GeneSpring GX 10
19 Simple and Advanced Pathway Analysis
20 Ingenuity Pathway Analysis (IPA) Plug-in Ingenuity Pathway Analysis (IPA) scripts can now be launched from a link in the Workflow browser Create Pathway in IPA Perform Data Analysis on Experiment Perform Data Analysis on Entity List List of genes from IPA can also be imported into GeneSpring GX
21 Data Migration
22 Automated GX 7 Migration Tool Step1: Prepare for GS7 Migration- tool automatically prepares data for migration Step3: Open Project with name corresponding to GX 7 genome to see the migrated data. Note that if genome was assigned a project in GX 7, this name will be the name of the project in GX 10 instead of the name of GX 7 genome Step2: Select GS7 genome to migrate to GS10- all experiments, samples, interpretation, gene lists, trees, parameter values, condition values, and classifications will be automatically migrated
23 Automatic GX 7 Data Migration When migration is finished running, a summary report is displayed Information for how many objects are supposed to be migrated versus how many were migrated is reported Each error is logged
24 Other New and Improved Features alternative splicing gene expression real-time PCR mirna pathway analysis
25 Technology Annotation, Data Organization, Import, and Export Options for creating and/or updating technology annotations: From Agilent Server From Agilent earray From GeneSpring Update file From Biological Genome From text file Support for.gpr files Addition of a My Favorites folder Copy/Paste export option in most result tables
26 Normalization and Filtering Options Normalization options: Normalize to control genes Scaling Baseline transformation to multiple control groups Filtering options: Filter on Volcano Plot (implemented as its own link in Workflow browser) Filter by Error (coefficient of variation and standard deviation) Filter on Data Files Filter by Expression (raw and normalized intensity values or percentile)
27 Data Visualization Hierarchical clustering trees Navigator view of entire tree Zoom capability to make navigation easy Color branches by parameter and show coloring blocks Mouse over to see degree of similarity and gene annotation Ability to extract sub-tree Mouse-over to get gene annotation in views Addition of fold-change lines to Scatter plot MvA plot
28 GeneSpring Workgroup 10
29 Changes in Workgroup 10 Version number changed to align with GeneSpring version number Pathway interaction database incorporated into Workgroup My Favorites Folder added to data hierarchy of Workgroup
30 GeneSpring GX 10 e-seminar Series Register for live e-seminars at Topics for scheduled e-seminars: Introduction to GeneSpring GX 10 New Features (Oct 1 st ) Joint Analysis of mirna and Gene Expression Data in GeneSpring GX (Oct 8th) Analysis of real-time PCR data in GeneSpring GX and Comparison to Microarray Results (Oct 22nd) Identifying Significant Differences in Alternative Splicing Events in GeneSpring GX (Oct 29th) Network Analysis in GeneSpring GX- Building Relevant Networks from Genes of Interest (Nov 5th)
Next-Generation Sequencing Gene Expression Analysis Using Agilent GeneSpring GX
Next-Generation Sequencing Gene Expression Analysis Using Agilent GeneSpring GX Technical Overview Introduction RNA Sequencing (RNA-Seq) is one of the most commonly used next-generation sequencing (NGS)
From Variants to Pathways: Agilent GeneSpring GX s Variant Analysis Workflow
From Variants to Pathways: Agilent GeneSpring GX s Variant Analysis Workflow Technical Overview Import VCF Introduction Next-generation sequencing (NGS) studies have created unanticipated challenges with
Agilent Genomics Software Future Directions
Agilent Genomics Software Future Directions Michael Rosenberg, PhD Director, Genomics Software Agilent: A Focused Measurement Company Serving Diverse End Markets Electronic Measurement 2008 Revenue: $3.6
Analysis of Microarray Data
Analysis of Microarray Data Lecture 3: Visualization and Functional Analysis George Bell, Ph.D. Senior Bioinformatics Scientist Bioinformatics and Research Computing Whitehead Institute Outline Review
Gene-Level Analysis of Exon Array Data using Partek Genomics Suite 6.6
Gene-Level Analysis of Exon Array Data using Partek Genomics Suite 6.6 Overview This tutorial will demonstrate how to: Summarize core exon-level data to produce gene-level data Perform exploratory analysis
Gene Expression Profiling and Validation Using Agilent SurePrint G3 Gene Expression Arrays
Gene Expression Profiling and Validation Using Agilent SurePrint G3 Gene Expression Arrays Application Note Authors Bahram Arezi, Nilanjan Guha and Anne Bergstrom Lucas Agilent Technologies Inc. Santa
Whole Transcriptome Analysis of Illumina RNA- Seq Data. Ryan Peters Field Application Specialist
Whole Transcriptome Analysis of Illumina RNA- Seq Data Ryan Peters Field Application Specialist Partek GS in your NGS Pipeline Your Start-to-Finish Solution for Analysis of Next Generation Sequencing Data
Gene Regulation Solutions. Microarrays and Next-Generation Sequencing
Gene Regulation Solutions Microarrays and Next-Generation Sequencing Gene Regulation Solutions The Microarrays Advantage Microarrays Lead the Industry in: Comprehensive Content SurePrint G3 Human Gene
Agilent Genomic Workbench 7.0
Agilent Genomic Workbench 7.0 Product Overview Guide Agilent Technologies Notices Agilent Technologies, Inc. 2012, 2015 No part of this manual may be reproduced in any form or by any means (including electronic
Gene Signal Estimates from Exon Arrays
Gene Signal Estimates from Exon Arrays I. Introduction: With exon arrays like the GeneChip Human Exon 1.0 ST Array, researchers can examine the transcriptional profile of an entire gene (Figure 1). Being
IPA Advanced Training Course
IPA Advanced Training Course Academia Sinica 2015 Oct Gene( 陳冠文 ) Supervisor and IPA certified analyst 1 Review for Introductory Training course Searching Building a Pathway Editing a Pathway for Publication
BCHM 6280 Tutorial: Gene specific information using NCBI, Ensembl and genome viewers
BCHM 6280 Tutorial: Gene specific information using NCBI, Ensembl and genome viewers Web resources: NCBI database: http://www.ncbi.nlm.nih.gov/ Ensembl database: http://useast.ensembl.org/index.html UCSC
Analysis of a Tiling Regulation Study in Partek Genomics Suite 6.6
Analysis of a Tiling Regulation Study in Partek Genomics Suite 6.6 The example data set used in this tutorial consists of 6 technical replicates from the same human cell line, 3 are SP1 treated, and 3
Analyzing Affymetrix GeneChip SNP 6 Copy Number Data in Partek
Analyzing Affymetrix GeneChip SNP 6 Copy Number Data in Partek This example data set consists of 20 selected HapMap samples, representing 10 females and 10 males, drawn from a mixed ethnic population of
Microarray Technique. Some background. M. Nath
Microarray Technique Some background M. Nath Outline Introduction Spotting Array Technique GeneChip Technique Data analysis Applications Conclusion Now Blind Guess? Functional Pathway Microarray Technique
Functional Enrichment Analysis & Candidate Gene Ranking
Functional Enrichment Analysis & Candidate Gene Ranking Anil Jegga Biomedical Informatics Contact Information: Anil Jegga Biomedical Informatics Room # 232, S Building 10th Floor CCHMC Homepage: http://anil.cchmc.org
Lecture #1. Introduction to microarray technology
Lecture #1 Introduction to microarray technology Outline General purpose Microarray assay concept Basic microarray experimental process cdna/two channel arrays Oligonucleotide arrays Exon arrays Comparing
CS 5984: Application of Basic Clustering Algorithms to Find Expression Modules in Cancer
CS 5984: Application of Basic Clustering Algorithms to Find Expression Modules in Cancer T. M. Murali January 31, 2006 Innovative Application of Hierarchical Clustering A module map showing conditional
user s guide Question 3
Question 3 During a positional cloning project aimed at finding a human disease gene, linkage data have been obtained suggesting that the gene of interest lies between two sequence-tagged site markers.
user s guide Question 3
Question 3 During a positional cloning project aimed at finding a human disease gene, linkage data have been obtained suggesting that the gene of interest lies between two sequence-tagged site markers.
Analysis of Microarray Data
Analysis of Microarray Data Lecture 1: Experimental Design and Data Normalization George Bell, Ph.D. Senior Bioinformatics Scientist Bioinformatics and Research Computing Whitehead Institute Outline Introduction
The first and only fully-integrated microarray instrument for hands-free array processing
The first and only fully-integrated microarray instrument for hands-free array processing GeneTitan Instrument Transform your lab with a GeneTitan Instrument and experience the unparalleled power of streamlining
Bioinformatics for Proteomics. Ann Loraine
Bioinformatics for Proteomics Ann Loraine aloraine@uab.edu What is bioinformatics? The science of collecting, processing, organizing, storing, analyzing, and mining biological information, especially data
Long and short/small RNA-seq data analysis
Long and short/small RNA-seq data analysis GEF5, 4.9.2015 Sami Heikkinen, PhD, Dos. Topics 1. RNA-seq in a nutshell 2. Long vs short/small RNA-seq 3. Bioinformatic analysis work flows GEF5 / Heikkinen
Introduction to gene expression microarray data analysis
Introduction to gene expression microarray data analysis Outline Brief introduction: Technology and data. Statistical challenges in data analysis. Preprocessing data normalization and transformation. Useful
Gene Expression Analysis Superior Solutions for any Project
Gene Expression Analysis Superior Solutions for any Project Find Your Perfect Match ArrayXS Global Array-to-Go Focussed Comprehensive: detect the whole transcriptome reliably Certified: discover exceptional
Analysis of Microarray Data
Analysis of Microarray Data Lecture 1: Experimental Design and Data Normalization George Bell, Ph.D. Senior Bioinformatics Scientist Bioinformatics and Research Computing Whitehead Institute Outline Introduction
measuring gene expression December 5, 2017
measuring gene expression December 5, 2017 transcription a usually short-lived RNA copy of the DNA is created through transcription RNA is exported to the cytoplasm to encode proteins some types of RNA
6. GENE EXPRESSION ANALYSIS MICROARRAYS
6. GENE EXPRESSION ANALYSIS MICROARRAYS BIOINFORMATICS COURSE MTAT.03.239 16.10.2013 GENE EXPRESSION ANALYSIS MICROARRAYS Slides adapted from Konstantin Tretyakov s 2011/2012 and Priit Adlers 2010/2011
Outline. Analysis of Microarray Data. Most important design question. General experimental issues
Outline Analysis of Microarray Data Lecture 1: Experimental Design and Data Normalization Introduction to microarrays Experimental design Data normalization Other data transformation Exercises George Bell,
Microarray Analysis of Gene Expression in Huntington's Disease Peripheral Blood - a Platform Comparison. CodeLink compatible
Microarray Analysis of Gene Expression in Huntington's Disease Peripheral Blood - a Platform Comparison CodeLink compatible Microarray Analysis of Gene Expression in Huntington's Disease Peripheral Blood
BABELOMICS: Microarray Data Analysis
BABELOMICS: Microarray Data Analysis Madrid, 21 June 2010 Martina Marbà mmarba@cipf.es Bioinformatics and Genomics Department Centro de Investigación Príncipe Felipe (CIPF) (Valencia, Spain) DNA Microarrays
Outline. Array platform considerations: Comparison between the technologies available in microarrays
Microarray overview Outline Array platform considerations: Comparison between the technologies available in microarrays Differences in array fabrication Differences in array organization Applications of
Bioinformatics Analysis of Nano-based Omics Data
Bioinformatics Analysis of Nano-based Omics Data Penny Nymark, Pekka Kohonen, Vesa Hongisto and Roland Grafström Hands-on Workshop on Nano Safety Assessment, 29 th September, 2016, National Technical University
Microarray Gene Expression Analysis at CNIO
Microarray Gene Expression Analysis at CNIO Orlando Domínguez Genomics Unit Biotechnology Program, CNIO 8 May 2013 Workflow, from samples to Gene Expression data Experimental design user/gu/ubio Samples
Hands-On Four Investigating Inherited Diseases
Hands-On Four Investigating Inherited Diseases The purpose of these exercises is to introduce bioinformatics databases and tools. We investigate an important human gene and see how mutations give rise
New Stringent Two-Color Gene Expression Workflow Enables More Accurate and Reproducible Microarray Data
Application Note GENOMICS INFORMATICS PROTEOMICS METABOLOMICS A T C T GATCCTTC T G AAC GGAAC T AATTTC AA G AATCTGATCCTTG AACTACCTTCCAAGGTG New Stringent Two-Color Gene Expression Workflow Enables More
ChroMoS Guide (version 1.2)
ChroMoS Guide (version 1.2) Background Genome-wide association studies (GWAS) reveal increasing number of disease-associated SNPs. Since majority of these SNPs are located in intergenic and intronic regions
Sanger vs Next-Gen Sequencing
Tools and Algorithms in Bioinformatics GCBA815/MCGB815/BMI815, Fall 2017 Week-8: Next-Gen Sequencing RNA-seq Data Analysis Babu Guda, Ph.D. Professor, Genetics, Cell Biology & Anatomy Director, Bioinformatics
Expand Your Research with Metabolomics and Proteomics. Christine Miller Omics Market Manager ASMS 2017
Expand Your Research with Metabolomics and Proteomics Christine Miller Omics Market Manager ASMS 2017 New Additions to Agilent Omics Workflows Acquisition Ion Mobility Q-TOF IM All Ions MS/MS Find Features
NCBI web resources I: databases and Entrez
NCBI web resources I: databases and Entrez Yanbin Yin Most materials are downloaded from ftp://ftp.ncbi.nih.gov/pub/education/ 1 Homework assignment 1 Two parts: Extract the gene IDs reported in table
Introduction to Bioinformatics and Gene Expression Technology
Vocabulary Introduction to Bioinformatics and Gene Expression Technology Utah State University Spring 2014 STAT 5570: Statistical Bioinformatics Notes 1.1 Gene: Genetics: Genome: Genomics: hereditary DNA
Host : Dr. Nobuyuki Nukina Tutor : Dr. Fumitaka Oyama
Method to assign the coding regions of ESTs Céline Becquet Summer Program 2002 Structural Neuropathology Lab Molecular Neuropathology Group RIKEN Brain Science Institute Host : Dr. Nobuyuki Nukina Tutor
Péter Antal Ádám Arany Bence Bolgár András Gézsi Gergely Hajós Gábor Hullám Péter Marx András Millinghoffer László Poppe Péter Sárközy BIOINFORMATICS
Péter Antal Ádám Arany Bence Bolgár András Gézsi Gergely Hajós Gábor Hullám Péter Marx András Millinghoffer László Poppe Péter Sárközy BIOINFORMATICS The Bioinformatics book covers new topics in the rapidly
FirePlex mirna Assay. Multiplex microrna profiling from low sample inputs
FirePlex mirna Assay Multiplex microrna profiling from low sample inputs Abstract We introduce a new assay for multiplex microrna (mirna) discovery and verification that enables simultaneous profiling
Gene Expression Technology
Gene Expression Technology Bing Zhang Department of Biomedical Informatics Vanderbilt University bing.zhang@vanderbilt.edu Gene expression Gene expression is the process by which information from a gene
Oncomine cfdna Assays Part III: Variant Analysis
Oncomine cfdna Assays Part III: Variant Analysis USER GUIDE for use with: Oncomine Lung cfdna Assay Oncomine Colon cfdna Assay Oncomine Breast cfdna Assay Catalog Numbers A31149, A31182, A31183 Publication
MicroRNA sequencing (mirnaseq)
, Robust experimental design Data analysis using the CAP-miRSeq: A comprehensive analysis pipeline for deep microrna sequencing E. Starr Hazard Over view of this first lecture 1) Review of very basic mirna
Using 2-way ANOVA to dissect gene expression following myocardial infarction in mice
Using 2-way ANOVA to dissect gene expression following myocardial infarction in mice Thank you for waiting. The presentation will be starting in a few minutes at 9AM Pacific Daylight Time. During this
Training materials.
Training materials Ensembl training materials are protected by a CC BY license http://creativecommons.org/licenses/by/4.0/ If you wish to re-use these materials, please credit Ensembl for their creation
Microarray Analysis of Gene Expression in Huntington's Disease Peripheral Blood - a Platform Comparison
Microarray Analysis of Gene Expression in Huntington's Disease Peripheral Blood - a Platform Comparison Thank you for waiting. The presentation will be starting in a few minutes at 9AM Pacific Daylight
DNA Microarray Technology
CHAPTER 1 DNA Microarray Technology All living organisms are composed of cells. As a functional unit, each cell can make copies of itself, and this process depends on a proper replication of the genetic
How to view Results with Scaffold. Proteomics Shared Resource
How to view Results with Scaffold Proteomics Shared Resource Starting out Download Scaffold from http://www.proteomes oftware.com/proteom e_software_prod_sca ffold_download.html Follow installation instructions
less sensitive than RNA-seq but more robust analysis pipelines expensive but quantitiatve standard but typically not high throughput
Chapter 11: Gene Expression The availability of an annotated genome sequence enables massively parallel analysis of gene expression. The expression of all genes in an organism can be measured in one experiment.
RT 2 Profiler PCR Array: Web-based data analysis tutorial
RT 2 Profiler PCR Array: Web-based data analysis tutorial.questions? Comments? or Suggestions?.Ask now or contact Technical Support.M F, 9 AM 6 PM EST..Telephone: 888-503-3187;.Email: support@sabiosciences.com.international
Biotechnology Explorer
Biotechnology Explorer C. elegans Behavior Kit Bioinformatics Supplement explorer.bio-rad.com Catalog #166-5120EDU This kit contains temperature-sensitive reagents. Open immediately and see individual
Guided tour to Ensembl
Guided tour to Ensembl Introduction Introduction to the Ensembl project Walk-through of the browser Variations and Functional Genomics Comparative Genomics BioMart Ensembl Genome browser http://www.ensembl.org
Examination Assignments
Bioinformatics Institute of India H-109, Ground Floor, Sector-63, Noida-201307, UP. INDIA Tel.: 0120-4320801 / 02, M. 09818473366, 09810535368 Email: info@bii.in, Website: www.bii.in INDUSTRY PROGRAM IN
UKB_WCSGAX: UK Biobank 500K Samples Processing by the Affymetrix 1 Research Services Laboratory
UKB_WCSGAX: UK Biobank 500K Samples Processing by the Affymetrix 1 Research Services Laboratory June, 2017 1 Now part of Thermo Fisher Scientific Contents Overview... 3 Facility... 3 Process overview...
Bioinformatics and Genomics: A New SP Frontier?
Bioinformatics and Genomics: A New SP Frontier? A. O. Hero University of Michigan - Ann Arbor http://www.eecs.umich.edu/ hero Collaborators: G. Fleury, ESE - Paris S. Yoshida, A. Swaroop UM - Ann Arbor
High Cross-Platform Genotyping Concordance of Axiom High-Density Microarrays and Eureka Low-Density Targeted NGS Assays
High Cross-Platform Genotyping Concordance of Axiom High-Density Microarrays and Eureka Low-Density Targeted NGS Assays Ali Pirani and Mohini A Patil ISAG July 2017 The world leader in serving science
Comp/Phys/APSc 715. Example Videos. Administrative 4/17/2014. Bioinformatics Visualization. Vis 2013, Schindler. Matlab bioinformatics toolbox
Comp/Phys/APSc 715 Bioinformatics Visualization Example Videos Vis 2013, Schindler Lagrangian coherent structures in flow Matlab bioinformatics toolbox http://www.mathworks.com/videos/bioinformatic s-toolbox-overview-61196.html
GS Analysis of Microarray Data
GS01 0163 Analysis of Microarray Data Keith Baggerly and Brad Broom Department of Bioinformatics and Computational Biology UT M. D. Anderson Cancer Center kabagg@mdanderson.org bmbroom@mdanderson.org 7
Genomic Data Analysis Services Available for PL-Grid Users
Domain-oriented services and resources of Polish Infrastructure for Supporting Computational Science in the European Research Space PLGrid Plus Domain-oriented services and resources of Polish Infrastructure
Nature Genetics: doi: /ng Supplementary Figure 1
Supplementary Figure 1 Processing of mutations and generation of simulated controls. On the left, a diagram illustrates the manner in which covariate-matched simulated mutations were obtained, filtered
WELCOME. Norma J. Nowak, PhD Executive Director, NY State Center of Excellence in Bioinformatics and Life Sciences (CBLS)
WELCOME Norma J. Nowak, PhD Executive Director, NY State Center of Excellence in Bioinformatics and Life Sciences (CBLS) Director, UB Genomics and Bioinformatics Core (GBC) o o o o o o o o o o o o Grow
reverse transcription! RT 1! RT 2! RT 3!
Supplementary Figure! Entire workflow repeated 3 times! mirna! stock! -fold dilution series! to yield - copies! per µl in PCR reaction! reverse transcription! RT! pre-pcr! mastermix!!!! 3!!! 3! ddpcr!
Introduction to Bioinformatics and Gene Expression Technologies
Introduction to Bioinformatics and Gene Expression Technologies Utah State University Fall 2017 Statistical Bioinformatics (Biomedical Big Data) Notes 1 1 Vocabulary Gene: hereditary DNA sequence at a
Chimp Sequence Annotation: Region 2_3
Chimp Sequence Annotation: Region 2_3 Jeff Howenstein March 30, 2007 BIO434W Genomics 1 Introduction We received region 2_3 of the ChimpChunk sequence, and the first step we performed was to run RepeatMasker
Analysis of Biological Sequences SPH
Analysis of Biological Sequences SPH 140.638 swheelan@jhmi.edu nuts and bolts meet Tuesdays & Thursdays, 3:30-4:50 no exam; grade derived from 3-4 homework assignments plus a final project (open book,
A Genomics (R)evolution: Harnessing the Power of Single Cells
A Genomics (R)evolution: Harnessing the Power of Single Cells Fundamental Question #1 If Transcriptional Heterogeneity ( Noise ) is so great in single cells What s the Point? Single Cells = True Biology
MassHunter Profinder: Batch Processing Software for High Quality Feature Extraction of Mass Spectrometry Data
MassHunter Profinder: Batch Processing Software for High Quality Feature Extraction of Mass Spectrometry Data Technical Overview Introduction LC/MS metabolomics workflows typically involve the following
Introduction to Microarray Analysis
Introduction to Microarray Analysis Methods Course: Gene Expression Data Analysis -Day One Rainer Spang Microarrays Highly parallel measurement devices for gene expression levels 1. How does the microarray
STATC 141 Spring 2005, April 5 th Lecture notes on Affymetrix arrays. Materials are from
STATC 141 Spring 2005, April 5 th Lecture notes on Affymetrix arrays Materials are from http://www.ohsu.edu/gmsr/amc/amc_technology.html The GeneChip high-density oligonucleotide arrays are fabricated
New Statistical Algorithms for Monitoring Gene Expression on GeneChip Probe Arrays
GENE EXPRESSION MONITORING TECHNICAL NOTE New Statistical Algorithms for Monitoring Gene Expression on GeneChip Probe Arrays Introduction Affymetrix has designed new algorithms for monitoring GeneChip
PrimeTime Pre-designed qpcr Assays
PrimeTime Pre-designed qpcr Assays nuclease assays for human, mouse, and rat PrimeTime qpcr Assays IDT now offers PrimeTime Pre-designed qpcr Assays that are guaranteed to work for human, mouse, and rat
SIMS2003. Instructors:Rus Yukhananov, Alex Loguinov BWH, Harvard Medical School. Introduction to Microarray Technology.
SIMS2003 Instructors:Rus Yukhananov, Alex Loguinov BWH, Harvard Medical School Introduction to Microarray Technology. Lecture 1 I. EXPERIMENTAL DETAILS II. ARRAY CONSTRUCTION III. IMAGE ANALYSIS Lecture
SMARTer Ultra Low RNA Kit for Illumina Sequencing Two powerful technologies combine to enable sequencing with ultra-low levels of RNA
SMARTer Ultra Low RNA Kit for Illumina Sequencing Two powerful technologies combine to enable sequencing with ultra-low levels of RNA The most sensitive cdna synthesis technology, combined with next-generation
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Supplementary Material
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions Joshua N. Burton 1, Andrew Adey 1, Rupali P. Patwardhan 1, Ruolan Qiu 1, Jacob O. Kitzman 1, Jay Shendure 1 1 Department
Exercise1 ArrayExpress Archive - High-throughput sequencing example
ArrayExpress and Atlas practical: querying and exporting gene expression data at the EBI Gabriella Rustici gabry@ebi.ac.uk This practical will introduce you to the data content and query functionality
GS Analysis of Microarray Data
GS01 0163 Analysis of Microarray Data Keith Baggerly and Kevin Coombes Department of Bioinformatics and Computational Biology UT M. D. Anderson Cancer Center kabagg@mdanderson.org kcoombes@mdanderson.org
EECS730: Introduction to Bioinformatics
EECS730: Introduction to Bioinformatics Lecture 14: Microarray Some slides were adapted from Dr. Luke Huan (University of Kansas), Dr. Shaojie Zhang (University of Central Florida), and Dr. Dong Xu and
Chromosome Analysis Suite 3.0 (ChAS 3.0)
Chromosome Analysis Suite 3.0 (ChAS 3.0) FAQs related to CytoScan Cytogenetics Suite 1. What is required for processing and viewing CytoScan array CEL files? CytoScan array CEL files are processed and
Gene Expression: Transcription
Gene Expression: Transcription The majority of genes are expressed as the proteins they encode. The process occurs in two steps: Transcription = DNA RNA Translation = RNA protein Taken together, they make
IPA : Maximizing the Biological Interpretation of Gene, Transcript & Protein Expression Data with IPA
IPA : Maximizing the Biological Interpretation of Gene, Transcript & Protein Expression Data with IPA Marisa Chen Account Manager Qiagen Advanced Genomics Marisa.Chen@qiagen.com (203) 500-1237 Dev Mistry,
Probe-Level Data Normalisation: RMA and GC-RMA Sam Robson Images courtesy of Neil Ward, European Application Engineer, Agilent Technologies.
Probe-Level Data Normalisation: RMA and GC-RMA Sam Robson Images courtesy of Neil Ward, European Application Engineer, Agilent Technologies. References Summaries of Affymetrix Genechip Probe Level Data,
UCSC Genome Browser. Introduction to ab initio and evidence-based gene finding
UCSC Genome Browser Introduction to ab initio and evidence-based gene finding Wilson Leung 06/2006 Outline Introduction to annotation ab initio gene finding Basics of the UCSC Browser Evidence-based gene
PCR Array FAQ s. PCR Arrays: Placing an order
PCR Array FAQ s PCR Arrays: Placing an order What PCR Array services does the facility provide? The DNA Analysis Facility provides support for gene expression studies using PCR Array technology from a
Introduction to Bioinformatics. Fabian Hoti 6.10.
Introduction to Bioinformatics Fabian Hoti 6.10. Analysis of Microarray Data Introduction Different types of microarrays Experiment Design Data Normalization Feature selection/extraction Clustering Introduction
Background Correction and Normalization. Lecture 3 Computational and Statistical Aspects of Microarray Analysis June 21, 2005 Bressanone, Italy
Background Correction and Normalization Lecture 3 Computational and Statistical Aspects of Microarray Analysis June 21, 2005 Bressanone, Italy Feature Level Data Outline Affymetrix GeneChip arrays Two
CS273B: Deep Learning in Genomics and Biomedicine. Recitation 1 30/9/2016
CS273B: Deep Learning in Genomics and Biomedicine. Recitation 1 30/9/2016 Topics Genetic variation Population structure Linkage disequilibrium Natural disease variants Genome Wide Association Studies Gene
Welcome to the NGS webinar series
Welcome to the NGS webinar series Webinar 1 NGS: Introduction to technology, and applications NGS Technology Webinar 2 Targeted NGS for Cancer Research NGS in cancer Webinar 3 NGS: Data analysis for genetic
QIAGEN s NGS Solutions for Biomarkers NGS & Bioinformatics team QIAGEN (Suzhou) Translational Medicine Co.,Ltd
QIAGEN s NGS Solutions for Biomarkers NGS & Bioinformatics team QIAGEN (Suzhou) Translational Medicine Co.,Ltd 1 Our current NGS & Bioinformatics Platform 2 Our NGS workflow and applications 3 QIAGEN s
Product Applications for the Sequence Analysis Collection
Product Applications for the Sequence Analysis Collection Pipeline Pilot Contents Introduction... 1 Pipeline Pilot and Bioinformatics... 2 Sequence Searching with Profile HMM...2 Integrating Data in a
PrimePCR Assay Validation Report
Gene Information Gene Name laminin, beta 3 Gene Symbol Organism Gene Summary Gene Aliases RefSeq Accession No. UniGene ID Ensembl Gene ID LAMB3 Human The product encoded by this gene is a laminin that
Genomic region (ENCODE) Gene definitions
DNA From genes to proteins Bioinformatics Methods RNA PROMOTER ELEMENTS TRANSCRIPTION Iosif Vaisman mrna SPLICE SITES SPLICING Email: ivaisman@gmu.edu START CODON STOP CODON TRANSLATION PROTEIN From genes
Quality Measures for CytoChip Microarrays
Quality Measures for CytoChip Microarrays How to evaluate CytoChip Oligo data quality in BlueFuse Multi software. Data quality is one of the most important aspects of any microarray experiment. This technical
DNA Microarray Data Oligonucleotide Arrays
DNA Microarray Data Oligonucleotide Arrays Sandrine Dudoit, Robert Gentleman, Rafael Irizarry, and Yee Hwa Yang Bioconductor Short Course 2003 Copyright 2002, all rights reserved Biological question Experimental
Bioinformatics III Structural Bioinformatics and Genome Analysis. PART II: Genome Analysis. Chapter 7. DNA Microarrays
Bioinformatics III Structural Bioinformatics and Genome Analysis PART II: Genome Analysis Chapter 7. DNA Microarrays 7.1 Motivation 7.2 DNA Microarray History and current states 7.3 DNA Microarray Techniques
BIOINFORMATICS AND SYSTEM BIOLOGY (INTERNATIONAL PROGRAM)
BIOINFORMATICS AND SYSTEM BIOLOGY (INTERNATIONAL PROGRAM) PROGRAM TITLE DEGREE TITLE Master of Science Program in Bioinformatics and System Biology (International Program) Master of Science (Bioinformatics