Healthy ControlCase 2D gel images of Serum protein sample Set of gel images for analysis.

Slides:

Advertisements

Similar presentations

Shibing Deng Pfizer, Inc. Efficient Outlier Identification in Lung Cancer Study.

Advertisements

Microarray technology and analysis of gene expression data Hillevi Lindroos.

CISC667, F05, Lec24, Liao1 CISC 667 Intro to Bioinformatics (Fall 2005) DNA Microarray, 2d gel, MSMS, yeast 2-hybrid.

Project 1 Frog Gels: Analysis of Skin John Donich Claudia Morales Kevin Berry.

Supplement Figure 1A. Representative 2D gel image of normal whey with 32 differently expressed protein spots identified by peptide mass fingerprinting.

SDS-PAGE gel analysis SDS-PAGE analysis is done to study the expression of a protein from the control and the sample, to detect the molecular weight of.

Analysis of microarray data

Classifier training FDR analysis Predictor discovery in training set 4 Training set SJIA (12 F, 12 Q) 1 DIGE raw gel images Matched samples SJIA (10 F,

2D-Gel Analysis Jennifer Wagner Image retrieved from

2007 GeneSpring MS GeneSpring for Metabolite BioMarker Analysis using Mass Spectrometry data Agilent Q-TOF VIP Visit Jan 16-17, 2007 Santa Clara, CA Thon.

DNA microarray technology allows an individual to rapidly and quantitatively measure the expression levels of thousands of genes in a biological sample.

Introduction to DNA Microarray Technology Steen Knudsen Uma Chandran.

ProteoRed Multicentric Experiment 5 2D electrophoresis analysis Salamanca, March, 2010.

Cathy Eng M.D., Salil Sethi M.D., George J.Chang, M.D., Miguel A. Rodriguez-Bigas, M.D., John M. Skibber, M.D., Jianjun Shen Ph.D., Jijiang Zhu Ph.D.,

ProtPlot – A Tissue Molecular Anatomy Program Java-based Data Mining Tool: Screen Shots **** DRAFT - undergoing revision **** Peter F. Lemkin, Ph.D. (1),

Analysis and Management of Microarray Data Previous Workshops –Computer Aided Drug Design –Public Domain Resources in Biology –Application of Computer.

Demonstration of 2 -DE gel analysis procedure Virtual proteomics laboratory IIT-Bombay.

Quantitative analysis of 2D gels Generalities. Applications Mutant / wild type Physiological conditions Tissue specific expression Disease / normal state.

Classifier training FDR analysis Predictor discovery in training set 4 Training set SJIA (12 F, 12 Q) 1 DIGE raw gel images Matched samples SJIA (10 F,

Figure SOM1. Functional roles of the genes affected in zmet2-m1 mutants. Although the genes localized on the intracellular membranes were slightly over-represented.

Analyzing Expression Data: Clustering and Stats Chapter 16.

ControlDrug treated 2D gel images of bacterial protein sample Set of gel images for analysis.

Gene expression. Gene Expression 2 protein RNA DNA.

NCode TM miRNA Analysis Platform Identifies Differentially Expressed Novel miRNAs in Adenocarcinoma Using Clinical Human Samples Provided By BioServe.

7-1C Areas and Perimeters of Similar Polygons What is the relationship between the perimeter ratios of similar figures and their similarity ratio? What.

Main Figures and Tables

Volume 63, Issue 2, Pages (February 2003)

Aberrant Levels of miRNAs in Bone Marrow Microenvironment and Peripheral Blood of Myeloma Patients and Disease Progression Weixin Wang, Meghan Corrigan-Cummins,

Figure S2 A B Log2 Fold Change (+/- cAMP) Transcriptome (9hr)

Genomic analysis: Toward a new approach in breast cancer management

Proteomic Analysis post Acute Spinal Cord Injury in human

Image from Gene-Chips (Micorrrays) Statistics for microarray analysis (SMA)

Volume 144, Issue 3, Pages e1 (March 2013)

M. Fu, G. Huang, Z. Zhang, J. Liu, Z. Zhang, Z. Huang, B. Yu, F. Meng

2-DE gel analysis Harini Chandra

Differential Expression of Circular RNAs in Glioblastoma Multiforme and Its Correlation with Prognosis Junle Zhu, Jingliang Ye, Lei Zhang, Lili Xia,

Proteomic Serum Profile of Fatigued Men Receiving Localized External Beam Radiation Therapy for Non-Metastatic Prostate Cancer Nada Lukkahatai, PhD,

Distinctive proliferative phase differences in gene expression in human myometrium and leiomyomata Hongbo Wang, MD, Mamatha Mahadevappa, PhD, Karen Yamamoto,

Computational Diagnostics

Diverse Transcriptional Programs Associated with Environmental Stress and Hormones in the Arabidopsis Receptor-Like Kinase Gene Family Lee Chae, Sylvia.

Volume 18, Issue 2, Pages (February 2003)

Set-1. Quiz-Bacterial protein gel analysis

Kenneth Song, Samir Hanash Gastroenterology

Volume 120, Issue 4, Pages (March 2001)

Analysis of differentially expressed proteins involved in hand, foot and mouth disease and normal sera L. Deng, H.-L. Jia, C.-W. Liu, K.-H. Hu, G.-Q.

Differential accumulation of substrates in vivo

Agnieszka Malcher, M. S. , Natalia Rozwadowska, Ph. D

Aberrant Levels of miRNAs in Bone Marrow Microenvironment and Peripheral Blood of Myeloma Patients and Disease Progression Weixin Wang, Meghan Corrigan-Cummins,

Gender differences in the bronchoalveolar lavage cell proteome of patients with chronic obstructive pulmonary disease Maxie Kohler, PhD, AnnSofi Sandberg,

Volume 140, Issue 1, Pages (January 2011)

Cluster Analysis in Bioinformatics

Covering the Cover Gastroenterology

HUWE1 regulates ubiquitination of Shoc2 and RAF-1.

Integrated protein co‐expression and differential expression across the ALS‐FTD disease continuum Integrated protein co‐expression and differential expression.

Proteomic analysis of individual human embryos to identify novel biomarkers of development and viability Mandy G. Katz-Jaffe, Ph.D., David K. Gardner,

Analysis of differentially expressed proteins involved in hand, foot and mouth disease and normal sera L. Deng, H.-L. Jia, C.-W. Liu, K.-H. Hu, G.-Q.

Volume 65, Issue 2, Pages (February 2004)

Volume 12, Issue 6, Pages (December 2003)

Volume 18, Issue 1, Pages (January 2017)

Pulmonary sarcoidosis is associated with exosomal vitamin D–binding protein and inflammatory molecules Maria-Jose Martinez-Bravo, PhD, Casper J.E. Wahlund,

Landscape of Long Noncoding RNAs in Psoriatic and Healthy Skin

Cluster analysis and pathway-based characterization of differentially expressed genes and proteins from integrated proteomics. Cluster analysis and pathway-based.

Molecular Therapy - Nucleic Acids

Changes in mRNA levels do not correlate with changes in protein levels in upf1Δ and xrn1Δ cells. Changes in mRNA levels do not correlate with changes in.

Differential gene expression in whole blood from SJIA patients and healthy controls. A. Data were normalized in Beadstudio using the "average" method and.

ANSWERS FOR QUIZ.

Figure 1. Profiles of the top 50 mRNA probes of the first gene signature identified in the South African cohort. ... Figure 1. Profiles of the top 50 mRNA.

Overlap between changes in de novo protein synthesis after p53- or miR-34a-induction. Overlap between changes in de novo protein synthesis after p53- or.

Differential protein, mRNA, lncRNA and miRNA regulation by p53.

Fig. 5. Vitamin B12 supplementation in the host altered the transcriptome of P. acnes in the skin microbiota. Vitamin B12 supplementation in the host altered.

Presentation transcript:

Healthy ControlCase 2D gel images of Serum protein sample Set of gel images for analysis

Steps followed in gel analysis 1) Set up Project 2) Detect and Quantify Spots 3) Analyze Expression Profiles 4) Present Results

ANALYSIS, RESULT AND DATA INTERPRETATION

Project Name Serum sample 2D-Gels for Analysis. Project Creation Date ………………. Author ………………. Description Healthy vs diseased patient Use internal Standard No Pool C\Users\XYZ Groups Control(1 image) Control - Healthy person 349spots transferred from fused image 97 spots cancelled Diseased (1 image) P.falciparum diseased serum sample 349 spots transferred from fused image 97 spots cancelled Vector Matching : Project Summary:

Profile Spot Information Control Diseased Spot ID : 1999 pI : 5.26 MW : 65.1kDal 3D view Spot ID : 2082 pI : 5.28 MW : 44.8kDal 3D view Control P.fal Fused 3D view 1. Project Summary:

pI index Molecular weight (kDal) 85 Spot ID: 2082 pI : 5.28 Mol. weight : 44.8 kDal Spot ID: 1999 pI : 5.26 Mol. weight : 65.2 kDal 3.Figure showing Molecular weight to pI

No. of spots showing up regulation Up regulation No. of folds (and above)No.of spots Up regulation x Folds or above 4.1. Differential expression : Up regulation

ABCDEF GHIJK Mean normalized value of group-Control(Healthy person) Mean normalized value of group 2 (P.falciparum diseased person) Ratio = 4.2. expression profile: Up regulation(8-10 folds up) -11 spots

Down Regulation No. of folds (and above)No. of spots No. of spots showing up regulation Down regulation x Folds or above 4.3.Differential expression : Down regulation

4.4.Expression profile: Down regulation (9-10 folds down) - 9 spots ABCDE FGHI Mean normalized value of group-Control(Healthy person) Ratio = Mean normalized value of group 2 (P.falciparum diseased person)

Hierarchical Cluster AnalysisHCL Tree It provides information about similarly expressed protein. It helps in finding correlated protein 5.Cluster Analysis

6. Scatter plot