DAVID Bioinformatics Web Site 2012 – 2015 David Huang, MD LMS/CCR/NCI

Slides:



Advertisements
Similar presentations
Feb 10, 2004 Team Talent Life Sciences: Model Systems for the protein folding problem Jason Crain University of Edinburgh IBM T.J. Watson Research Center.
Advertisements

The gp41 fragment (purple) consists of a cytoplasmic tail and a hydrophobic membrane-spanning domain and is joined with the larger gp120 component (blue.
Course Code Course Title Credits BMS 500 Responsible Conduct of Research 1 BMS 510F Biochemistry and Cell Biology 10 BMS 512 Critical Thinking 1 BMS 523A.
Computational Diagnostics We are a new research group in the department of Computational Molecular Biology at the Max Planck Institute for Molecular Genetics.
Antibody structure Heavy chain constant region determines antibody class.
4.A.3 Cell Specialization Interactions between external stimuli and regulated gene expression result in specialization of cells, tissues and organs.
27803::Systems Biology1CBS, Department of Systems Biology Schedule for the Afternoon 13:00 – 13:30ChIP-chip lecture 13:30 – 14:30Exercise 14:30 – 14:45Break.
Transforming Growth Factor β Receptor Type II Tina Morris
Schedule for the Afternoon 13:00 – 13:30ChIP-chip lecture 13:30 – 14:30Exercise 14:30 – 14:45Break 14:45 – 15:15Regulatory pathways lecture 15:15 – 15:45Exercise.
Evaluation of Signaling Cascades Based on the Weights from Microarray and ChIP-seq Data by Zerrin Işık Volkan Atalay Rengül Çetin-Atalay Middle East Technical.
Phylogeny in Drug Discovery?
The role of PI3K signaling pathways in HIV-1 infection of resting CD4+T-cells Suha Saleh, Paul Cameron, Georgina Sallmann, Anthony Jaworowski, and Sharon.
The Myc Transcription Factor
Shankar Subramaniam University of California at San Diego Data to Biology.
Methods MHC class-I T cell epitope prediction for Nef Consensus and ancestral sequences of the Nef protein for the different HIV-1 subtypes were obtained.
A scenario for a genetically controlled fission of artificial vesicles E. Boenzli 1, M. Hadorn 1, M. G. Jørgensen 2, P. Eggenberger Hotz 3, M. M. Hanczyc.
2003 Inferring Connection Maps from AfCS Experimental Data and Legacy Data.
Signaling Pathways That Control Gene Activity TGFβ Receptors and the Direct Activation of Smads Presented By: Todd Lindsey.
P-1 Genetically controlled fusion, exocytosis and fission of artificial vesicles E. Boenzli 1, M. Hadorn 1, D. de Lucrezia 2, M. G. Jørgensen 3, P. Eggenberger.
Aphids evolved novel secreted proteins for symbiosis with bacterial endosymbiont by Shuji Shigenobu, and David L. Stern Proceedings B Volume 280(1750):
SRI International Bioinformatics 1 Object Groups & Enrichment Analysis Suzanne Paley Pathway Tools Workshop 2010.
Supplemental figure 1: Correlation coefficients between signal intensities from biological replicates of wild.
Gene Expression Data Analysis Lab Session CAD course Jian Li
Network & Systems Modeling 29 June 2009 NCSU GO Workshop.
Read Lab Dynamics of Complex Biochemical Systems Read Lab Dynamics of Complex Biochemical Systems
Leveraging Ontologies for Human Immunology Research Barry Smith, Alexander Diehl, Anna- Maria Masci Presented at Leveraging Standards and Ontologies to.
The RNA-Binding Protein KSRP Promotes Decay of  -Catenin mRNA and Is Inactivated by PI3K-AKT Signaling Roberto Gherzi et al. PLoS Biol. (2006)
Integrating the Bioinformatic Technology Group into your research programme Introduction People and Skills Examples Integrating the BTG Contacts BHRC Away.
The ‘regulates’ relationships Chris, David, Tanya.
DAVID R. SMITH DR. MARY DOLAN DR. JUDITH BLAKE Integrating the Cell Cycle Ontology with the Mouse Genome Database.
Control of Gene Expression
Bioinformatics lectures at Rice University Li Zhang Lecture 9: Networks and integrative genomic analysis
Genetically controlled fusion, exocytosis and fission of artificial vesicles E. Boenzli 1, M. Hadorn 1, D. de Lucrezia 2, M. G. Jørgensen 3, P. Eggenberger.
2003 Inferring Connection Maps from AfCS Experimental Data and Legacy Data.
Ontology based analyses methods ++ develop a grammar for making productions using mf, bp, cl: –derive a higher level grammar for next level of productions.
Control of Gene Expression Year 13 Biology. Exceptions to the usual Protein Synthesis Some viruses contain RNA and no DNA. RNA is therefore replicated.
Data provenance in biomedical discovery Donald Dunbar Queen’s Medical Research Institute University of Edinburgh Workshop on Principles of Provenance in.
Mutations on the V3 loop of gp120 may predict progression to AIDS Derese Getnet, Dr. Rebecca Roberts, Structural Biology, Ursinus College, Collegeville.
Figure 18.1 Comparing the size of a virus, a bacterium, and a eukaryotic cell.
Copyright OpenHelix. No use or reproduction without express written consent1.
The Central Dogma The Central Dogma traces the flow of genetic information DNA Replication, Transcription, and Translation take place in human cells as.
Retroviral Gene Therapy. What is Gene Therapy? Gene Therapy Strategies.
Non-Coding RNA Helen Nordquist November 13, 2015.
Structure of V3-containing HIV-1 gp120 core Huang, C. C., Tang, M., Zhang, M. Y., Majeed, S., Montabana, E., Stanfield, R. L., Dimitrov, D. S., Korber,
Pathway Informatics 30 th March, 2016 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University.
Large black circles: query genes grey circles: interacting or related proteins Light grey line: consolidated pathways Yellow: predicted pathways Green:
Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline Markham RB, Wang WC, Weisstein AE, Wang Z, Munoz A, Templeton A,
A New Statistical Method for Analyzing Longitudinal Multifactor Expression Data and It ’ s Application to Time Course Burn Data Baiyu Zhou Department of.
Journal Club Presentation BIOL368/F16: Bioinformatics Laboratory
محاضرة عامة التقنيات الحيوية (هندسة الجينات .. مبادئ وتطبيقات)
PABIO 590B Advanced Topics in Bioinformatics
Pathogenic mechanisms of B-lymphocyte dysfunction in HIV disease
Pathweavers Elizabeth McClellan Ribble, Ph.D.
Neural stem cells at sleep: Selective inhibition of orexin 2 receptor in mouse cortical neural stem cells increases proliferation and differentiation toward.
KEY CONCEPT Entire genomes are sequenced, studied, and compared.
Nat. Rev. Endocrinol. doi: /nrendo
Polydactyly L.A. Lettice, et al. Proc. Natl. Acad. Sci. USA 2002; 99(11):
KEY CONCEPT Entire genomes are sequenced, studied, and compared.
IRF4 regulates cytokine receptor expression in CD8+ T cells.
Schedule for the Afternoon
Structure of V3-containing HIV-1 gp120 core
Translated by Krishna Karamsetty
Linkage of ubiquitin system between plant and mammalian
Compare & Contrast Cells and Viruses
Molecular virology and immunology of HIV infection
Fig. 3 Conserved genomic association of PRC1 activity in different leukemic cells. Conserved genomic association of PRC1 activity in different leukemic.
Identification of aging-related genes and affected biological processes. Identification of aging-related genes and affected biological processes. (A) Experimental.
and Other Unstable mRNAs
Presentation transcript:

DAVID Bioinformatics Web Site 2012 – 2015 David Huang, MD LMS/CCR/NCI

The HIV-1 envelope protein gp120 impairs B cell proliferation by inducing TGF-β1 production and FcRL4 expression. Nature Immunology 14, 1256–1265 (2013) HIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication. Proc Natl Acad Sci U S A. 9;99(14): (2002) Exampled Studies: DAVID Manuals: Extracting biological meaning from large gene lists with DAVID Current Protocols in Bioinformatics, UNIT (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Nature Protocols 4, (2009)

Enrichment Analysis Red ball NOT enriched Red balls are enriched 10% 40%

Demonstration  Gene Centric Analysis  Annotation Centric Analysis  Pathway View