Under the guidance of  :- Mr. Pramod Katara   Presented by  :-   Supriya Karkra Ganga Jeena Ishu Sharma Mugdha Agarwal Pre...
<ul><li>Contents </li></ul><ul><li>Introduction </li></ul><ul><li>Objective </li></ul><ul><li>Review of Literature </li></...
Introduction
Genome <ul><li>Our genome encodes an enormous amount of information about our beings . </li></ul>
<ul><li>Genomics   </li></ul><ul><li>recent scientific discipline that strives to define and characterize the complete gen...
<ul><li>Regulatory Genomics  :   Genome-wide study of  gene regulation. </li></ul><ul><li>Regulatory Elements   :  </li></...
<ul><li>Mycobacterium tuberculosis. </li></ul><ul><li>Weakly gram-positive. </li></ul><ul><li>Human pathogen. </li></ul><u...
<ul><li>Objectives  </li></ul><ul><li>Prediction of the upstream region  of virulence genes. </li></ul><ul><li>Identificat...
Review of Literature
<ul><li>Cluster analysis is often used to infer regulatory modules or biological function by associating unknown genes wit...
Materials  and  Methodology
<ul><ul><ul><ul><ul><li>Stanford Microarray Database (SMD). </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>The inst...
Search for Virulent Genes P.syringae  Pv.  tomato  DC3000 M.tuberculosis  H37Rv Domain of Virulent Genes Domain of Virulen...
Results
 
 
 
 
<ul><li>Comparing the results for both the bacteria, we found most of the clusters with size of upstream regions in range ...
Some important References <ul><li>Jacques van Helden, Alma. F. Rios, and Julio Collado-Vides (2000). </li></ul><ul><ul><li...
http://genome –www5.stanford.edu/ http://www.tigr.org/ http://rana.lbl.gov/ http://www.mgc.ac.cn/VFs/ http://rsat.ulb.ac.b...
THANKS
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Prediction Of Regulatory Elements

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Cluster analysis of gene expression data, is
often used to infer regulatory modules or biological function by associating
unknown genes with other well known genes that have similar expression
patterns. Using simple clustering algorithm for microarray datasets we
grouped those genes that are very similar at expression level, and then
analyzed them for the prediction of regulatory elemetns by using RSAT.

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Prediction Of Regulatory Elements

  1. 1. Under the guidance of :- Mr. Pramod Katara Presented by :- Supriya Karkra Ganga Jeena Ishu Sharma Mugdha Agarwal Prediction of Regulatory Elements for Pathogenic Genes of P. syringae Pv. tomato DC3000 and M. tuberculosis H37Rv.
  2. 2. <ul><li>Contents </li></ul><ul><li>Introduction </li></ul><ul><li>Objective </li></ul><ul><li>Review of Literature </li></ul><ul><li>Materials and Methodology </li></ul><ul><li>Results </li></ul><ul><li>Conclusion and Further Aspects </li></ul><ul><li>References </li></ul>
  3. 3. Introduction
  4. 4. Genome <ul><li>Our genome encodes an enormous amount of information about our beings . </li></ul>
  5. 5. <ul><li>Genomics </li></ul><ul><li>recent scientific discipline that strives to define and characterize the complete genetic makeup of an organism . </li></ul>
  6. 6. <ul><li>Regulatory Genomics : Genome-wide study of gene regulation. </li></ul><ul><li>Regulatory Elements : </li></ul><ul><li>-Promoters. </li></ul><ul><li>-Transcription factor binding sites. </li></ul>
  7. 7. <ul><li>Mycobacterium tuberculosis. </li></ul><ul><li>Weakly gram-positive. </li></ul><ul><li>Human pathogen. </li></ul><ul><li>Pseudomonas syringae </li></ul><ul><li>Gram-negative bacterium. </li></ul><ul><li>Plant pathogen. </li></ul>Bacteria Under study…..
  8. 8. <ul><li>Objectives </li></ul><ul><li>Prediction of the upstream region of virulence genes. </li></ul><ul><li>Identification of regulatory elements pattern in virulence genes. </li></ul>
  9. 9. Review of Literature
  10. 10. <ul><li>Cluster analysis is often used to infer regulatory modules or biological function by associating unknown genes with other genes that have similar expression patterns and known regulatory elements or functions (Yeung et. al., 2004) </li></ul><ul><li>Clustering genes according to the similarity of their transcriptional response provides a direct hint to the regulons of the different transcription factors, many of which have still not been characterized (Jacques van Helden et. al., 2000). </li></ul><ul><li>Knowledge of the identity of a mediating TF can give important insights into the function of a gene via inference of the processes or conditions that lead to expression (Lenhard B et. al., 2003). </li></ul><ul><li>Analyzing gene expression data helps to discover co-regulated genes. Genes with similar patterns of mRNA expression and with similar functions are likely to be regulated via the same mechanism i.e more likely to have their promoter regions bound by a common transcription factor (Dominic et. al., 2004). </li></ul>
  11. 11. Materials and Methodology
  12. 12. <ul><ul><ul><ul><ul><li>Stanford Microarray Database (SMD). </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>The institute of genomic research (TIGR). </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>Virulence factor database (VFDB). </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>Pathogenicity island database (PAIDB). </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>GenBank. </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>Journals. </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>Gene Cluster. </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>Regulatory Sequence Analysis Tool (RSAT). </li></ul></ul></ul></ul></ul>DATA SOURCES: TOOLS/SOFTWARE:
  13. 13. Search for Virulent Genes P.syringae Pv. tomato DC3000 M.tuberculosis H37Rv Domain of Virulent Genes Domain of Virulent Genes SMD Data Clusters Phlyogenetic Tree Clusters Clusters of Probable virulence genes RSAT Upstream region Oligo-nucleotides Spaced Dyads
  14. 14. Results
  15. 19. <ul><li>Comparing the results for both the bacteria, we found most of the clusters with size of upstream regions in range of 50- 500. </li></ul><ul><li>Genes of the same cluster and clusters with same patterns are most likely to be regulated by same regulatory elements . </li></ul><ul><li>As compared to P.syringae , M. tuberculosis was found to have more number of dyad patterns than oligo-patterns. </li></ul><ul><li>By utilizing the information about the gene expression pattern of the whole genome and analysis of regulatory sites and their respective binding molecules i.e. TF, which are mainly responsible for regulation of genes, we can understand the mechanism of virulent genes and co-expressed genes responsible for causing the disease. </li></ul><ul><li>Gene expression pattern may also provide the way to create gene regulatory networks which may facilitate the chance to understand various proteins translated by pathogenic genes of </li></ul><ul><li>M. tuberculosis and P. syringae. </li></ul>Conclusions and Further Aspects...
  16. 20. Some important References <ul><li>Jacques van Helden, Alma. F. Rios, and Julio Collado-Vides (2000). </li></ul><ul><ul><li>Discovering regulatory elements in non-coding sequences by </li></ul></ul><ul><li>analysis of spaced dyads. Nucleic Acids Research. 28(8): 1808–1818. </li></ul><ul><li>Lenhard B, Albin S, Luis M, Pär E, Niclas J and Wyeth W(2003). </li></ul><ul><ul><li>Identification of conserved regulatory elements by comparative genome </li></ul></ul><ul><ul><li>analysis. Journal of Biology ; 2: 13doi:10.1186/1475-4924-2-13. </li></ul></ul><ul><li>Dominic J A, Isaac S, and Atul J (2004) . Quantifying the relationship </li></ul><ul><ul><li>between co-expression, co-regulation and gene function. </li></ul></ul><ul><ul><li>BMC Bioinformatics ; 5: 18. </li></ul></ul><ul><li>Yueyi L, Liping W, Serafim B, Douglas L, Brutlag, Liu J S, and Shirley L X. </li></ul><ul><li>(2004). A suite of web-based programs to search for transcriptional </li></ul><ul><li>regulatory motifs. Nucleic Acids Res; 32: 204–207. </li></ul><ul><li>Yenug Y K, Medvedovic M, and Bumgarner E R (2004). From co- expression </li></ul><ul><li>to co-regulation: how many microarray experiments do we need? </li></ul><ul><li>Genome biology ; 5: 48. </li></ul>
  17. 21. http://genome –www5.stanford.edu/ http://www.tigr.org/ http://rana.lbl.gov/ http://www.mgc.ac.cn/VFs/ http://rsat.ulb.ac.be/rsat/ http://www.phylogeny.fr/ http://ncbi.nlm.nih.gov/ URL References :
  18. 22. THANKS

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