Ce diaporama a bien été signalé.
Nous utilisons votre profil LinkedIn et vos données d’activité pour vous proposer des publicités personnalisées et pertinentes. Vous pouvez changer vos préférences de publicités à tout moment.

Bioinformatics in a Nutshell

1 580 vues

Publié le

Bioinformatics in a Nutshell
Predictive Analtyics and Data Science Conference, Bangkok Thailand May 27-28
Pravech Ajawatanawong, Ph. D

Publié dans : Données & analyses
  • DOWNLOAD FULL BOOKS, INTO AVAILABLE FORMAT ......................................................................................................................... ......................................................................................................................... ,DOWNLOAD FULL. PDF EBOOK here { https://tinyurl.com/yyxo9sk7 } ......................................................................................................................... ,DOWNLOAD FULL. EPUB Ebook here { https://tinyurl.com/yyxo9sk7 } ......................................................................................................................... ,DOWNLOAD FULL. doc Ebook here { https://tinyurl.com/yyxo9sk7 } ......................................................................................................................... ,DOWNLOAD FULL. PDF EBOOK here { https://tinyurl.com/yyxo9sk7 } ......................................................................................................................... ,DOWNLOAD FULL. EPUB Ebook here { https://tinyurl.com/yyxo9sk7 } ......................................................................................................................... ,DOWNLOAD FULL. doc Ebook here { https://tinyurl.com/yyxo9sk7 } ......................................................................................................................... ......................................................................................................................... ......................................................................................................................... .............. Browse by Genre Available eBooks ......................................................................................................................... Art, Biography, Business, Chick Lit, Children's, Christian, Classics, Comics, Contemporary, Cookbooks, Crime, Ebooks, Fantasy, Fiction, Graphic Novels, Historical Fiction, History, Horror, Humor And Comedy, Manga, Memoir, Music, Mystery, Non Fiction, Paranormal, Philosophy, Poetry, Psychology, Religion, Romance, Science, Science Fiction, Self Help, Suspense, Spirituality, Sports, Thriller, Travel, Young Adult,
       Répondre 
    Voulez-vous vraiment ?  Oui  Non
    Votre message apparaîtra ici
  • If you just broke up with your Ex,you have to follow these steps to get her back or risk ruining your chances. Click here ♥♥♥ http://ow.ly/mOLD301xGxr
       Répondre 
    Voulez-vous vraiment ?  Oui  Non
    Votre message apparaîtra ici
  • DOWNLOAD FULL BOOKS, INTO AVAILABLE FORMAT ......................................................................................................................... ......................................................................................................................... 1.DOWNLOAD FULL. PDF EBOOK here { https://tinyurl.com/y3nhqquc } ......................................................................................................................... 1.DOWNLOAD FULL. EPUB Ebook here { https://tinyurl.com/y3nhqquc } ......................................................................................................................... 1.DOWNLOAD FULL. doc Ebook here { https://tinyurl.com/y3nhqquc } ......................................................................................................................... 1.DOWNLOAD FULL. PDF EBOOK here { https://tinyurl.com/y3nhqquc } ......................................................................................................................... 1.DOWNLOAD FULL. EPUB Ebook here { https://tinyurl.com/y3nhqquc } ......................................................................................................................... 1.DOWNLOAD FULL. doc Ebook here { https://tinyurl.com/y3nhqquc } ......................................................................................................................... ......................................................................................................................... ......................................................................................................................... .............. Browse by Genre Available eBooks ......................................................................................................................... Art, Biography, Business, Chick Lit, Children's, Christian, Classics, Comics, Contemporary, Cookbooks, Crime, Ebooks, Fantasy, Fiction, Graphic Novels, Historical Fiction, History, Horror, Humor And Comedy, Manga, Memoir, Music, Mystery, Non Fiction, Paranormal, Philosophy, Poetry, Psychology, Religion, Romance, Science, Science Fiction, Self Help, Suspense, Spirituality, Sports, Thriller, Travel, Young Adult,
       Répondre 
    Voulez-vous vraiment ?  Oui  Non
    Votre message apparaîtra ici
  • DOWNLOAD FULL BOOKS, INTO AVAILABLE FORMAT ......................................................................................................................... ......................................................................................................................... 1.DOWNLOAD FULL. PDF EBOOK here { https://tinyurl.com/y3nhqquc } ......................................................................................................................... 1.DOWNLOAD FULL. EPUB Ebook here { https://tinyurl.com/y3nhqquc } ......................................................................................................................... 1.DOWNLOAD FULL. doc Ebook here { https://tinyurl.com/y3nhqquc } ......................................................................................................................... 1.DOWNLOAD FULL. PDF EBOOK here { https://tinyurl.com/y3nhqquc } ......................................................................................................................... 1.DOWNLOAD FULL. EPUB Ebook here { https://tinyurl.com/y3nhqquc } ......................................................................................................................... 1.DOWNLOAD FULL. doc Ebook here { https://tinyurl.com/y3nhqquc } ......................................................................................................................... ......................................................................................................................... ......................................................................................................................... .............. Browse by Genre Available eBooks ......................................................................................................................... Art, Biography, Business, Chick Lit, Children's, Christian, Classics, Comics, Contemporary, Cookbooks, Crime, Ebooks, Fantasy, Fiction, Graphic Novels, Historical Fiction, History, Horror, Humor And Comedy, Manga, Memoir, Music, Mystery, Non Fiction, Paranormal, Philosophy, Poetry, Psychology, Religion, Romance, Science, Science Fiction, Self Help, Suspense, Spirituality, Sports, Thriller, Travel, Young Adult,
       Répondre 
    Voulez-vous vraiment ?  Oui  Non
    Votre message apparaîtra ici

Bioinformatics in a Nutshell

  1. 1. Pravech Ajawatanawong, Ph.D. Department of Microbiology Faculty of Science Mahidol University Wisdom of the Land Mahidol University BIOINFORMATICS in a Nutshell
  2. 2. Biology Is Extremely Complex, Indeed!!! “… We think that physics is complicated because it is hard for us to understand, and because physics books are full of difficult mathematics. But the objects that physicists study are still basically simple objects. … The objects and phenomena that a physic book describes are simpler than a single cell in the body of its author. …”
  3. 3. Hierarchy of Organization molecule (chlorophyll) organelle (chloroplast) cell (plant cell) organ (leave) tissue (plant epithelial) organism (maple tree) population (maple population) ecosystem biome
  4. 4. Amazing of Organization
  5. 5. Emergent Properties molecule (chlorophyll) organelle (chloroplast) cell (plant cell) organ (leave) tissue (plant epithelial) organism (maple tree) population (maple population) ecosystem biome “Each level of biological organization has emergent properties.” We know very little about the whole biology.
  6. 6. Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics, and engineering to study and process biological data. — Wikipedia — Bioinformatics derives knowledge from computer analysis of biological data. These can consist of the information stored in the genetic code, but also experimental results from various sources, patient statistics, and scientific literature. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics is a rapidly developing branch of biology and is highly interdisciplinary, using techniques and concepts from informatics, statistics, mathematics, chemistry, biochemistry, physics, and linguistics. It  has many practical applications in different areas of biology and medicine. — Michael Nilges & Jens P. Linge, Institut Pasteur — What is Bioinformatics?
  7. 7. Bioinformatics in My Opinion!!! Bioinformatics is an interdisciplinary subject that uses knowledges and techniques from computer science, mathematics, statistics, information technologies and linguistics to get some informations from the massive biological data. Synonyms of BIOINFORMATICS computational biology biocomputing computational molecular biology
  8. 8. Computer Scientist Biologist Bioinformatics ≠ Computer + Biology Bioinformatician Bioinformaticians are the bridge between these groups
  9. 9. Central Dogma How information flow? Ref: http://genius.com/Biology-genius-the-central-dogma-annotated
  10. 10. DNA = Coca Cola phosphoric acidphosphate backbone sugardeoxyribose waterwater caffeineA, T, C and G
  11. 11. Sequence = Strings DNA = {A, T, C, G} protein = {A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y} RNA = {A, U, C, G} CATCAGCTCCACGCATCAGCGACTACACATTCGACTCAGCATCGACTACGCATCAGCTCCACGCATCAGCGACT ACACATTCGACTCAGCATCGACTACGCATCAGCTCCACGCATCAGCGACTACACATTCGACTCAGCATCGACTA CGCATCAGCTCCACGCATCAGCGACTACACATTCGACTCAGCATCGACTACGCATCAGCTCCACGCATCAGCGA CTACACATTCGACTCAGCATCGACTACGCATCAGCTCCACGCATCAGCGACTACACATTCGACTCAGCATGACT MSFQDIQQSEHFLLRPSEKVQKLETSQWPLLLKNFDKLNVLTNHYVPIPSGCSPLKRSIEDYVKSGFINLDKPA NPSSHEVVAWAKRILKVDKTGHSGTLDPKVTGCLIVCIERATRLVKSQQGAGKEYVCIFHLHSPVEDEQKVAKN IERLTGALFQRPPLISAVKRQLRVRTVYESKMLEYDKDKGMGVFWVSCEAGTYIRTMCVHLGLFLGVGGQMQEL RRVRSGINSEKEGLVTMHDILDAQWLYENHKDESYLRRAIKPLEALLTSHKRVIMKDTAVNALCYGAKIMLPGV
  12. 12. Main Types of Biological Data Sequence Data Structural Data Profile Data
  13. 13. (Some) Areas of Bioinformatics Biodatabase Sequence Analysis Structural Bioinformatics Microarray Data Analysis Systems Biology
  14. 14. Biodatabase
  15. 15. Why Biologists Needs Database?
  16. 16. PubMed
  17. 17. The World Largest Biodatabases http://www.ncbi.nlm.nih.gov
  18. 18. Ref: http://www.nlm.nih.gov/about/2015CJ.html Growth of GenBank
  19. 19. PDBJ
  20. 20. KEGG Database
  21. 21. Pfam Database
  22. 22. Sequence Analysis—a rosetta stone of life “SEQUENCE ANALYSIS is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution.” — Wikipedia —
  23. 23. Charles Darwin 1809–1882 Darwin also spent much time thinking about geology. De- spite bouts of seasickness, he read Lyell’s Principles of Geology isms that enhance their survival and reproduction in specific environments. Later, as he reassessed his observations, he be- PACIFIC OCEANPinta Genovesa The Galápagos Islands EquatorMarchena Fernandina Pinzón Santa Fe San Cristobal Florenza Isabela Santa Cruz Daphne Islands Santiago Española 0 4020 Kilometers ATLANTIC OCEAN PACIFIC OCEAN NORTH AMERICA Darwin in 1840, after his return from the voyage SOUTH AMERICA Great Britain AndesMtns. Cape Horn Cape of Good Hope Brazil Argentina Chile Equator Malay Archipelago AFRICA EUROPE HMS Beagle in port Tasmania AUSTRALIA New Zealand PACIFIC OCEAN ᭡ Figure 22.5 The voyage of HMS Beagle. His Voyage with HMS Beagle
  24. 24. On the Origin of Species “… It is a truly wonderful fact—the wonder of which we are apt to overlook from familiarity—that all animals and all plants throughout all time and space should be related to each other in group subordinate to group, in the manner which we everywhere behold namely, varieties of the same species most closely related together, species of the same genus less closely and unequally related together, forming sections and sub-genera, species of distinct genera much less closely related, and genera related in different degrees, forming sub- families, families, orders, subclasses, and classes. …” — Charles Darwin —
  25. 25. Darwin’s Tree
  26. 26. Visualization of Phylogeny shorter than 250 amino acid residues were discarded because they are too short for reliable control trees. All proteins in the resulting clusters are re- ferred to here as seed orthologs. Figure 6. Evolutionary relationships among the 35 eukaryotes used in this thesis (Hejnol et al., 2009; Parfrey et al., 2010). Ajawatanawong P. (2014) Mine the gaps, Uppsala University.
  27. 27. Carl Richard Woese 1928–2012 professor of microbiology at the University of Illinois at Urbana– Champaign famous for defining the Archaea by using 16S rRNA phylogeny originated the idea of RNA world hypothesis
  28. 28. SSU rDNA Structure of Bacteria
  29. 29. SSU—Ideal Molecular Marker Nucleic acid sequencing—16S rRNA gene (rDNA), oligonucleotide signature (e.g. indels) Since genome sequencing becomes cheaper, bacterial systematic using genome-based method is coming
  30. 30. Norman R Pace
  31. 31. Deep Evolution of Bacteria Aquificae Thermotogae Chloroflexi Deinococcus-Thermus Thermophiles Archaea Thermophilic (optimum temperature around 85ºC) paraphyletic group non-peptidoplycan cell wall similar to Archaea
  32. 32. Bacteria with Photosynthesis Chloroflexi Firmicutes Archaea Cyanobacteria Chlorobi α-proteobacteria PhotosyntheticBacteria γ-proteobacteria green non-sulfur bacteria heliobacteria cyanobacteria green sulfur bacteria purple sulfur bacteria β-proteobacteria purple non-sulfur bacteria purple non-sulfur bacteria
  33. 33. Proteobacteria β-proteobacteria γ-proteobacteria Archaea ε-proteobacteria δ-proteobacteria α-proteobacteria Proteobacteria Proteus—God of the Ocean
  34. 34. Gram Positive Bacteria Actinobacteria Firmicutes Gram Positive Bacteria Jim Henson
  35. 35. Genome Is a Book of Life ATTCGACTCAGCATCGACTACGCATCAGCTCCACGCATCAG CGACTACACATTCGACTCAGCATCGACTACGCATCAGCTCC ACGCATCAGCGACTACACATTCGACTCAGCATCGACTACGC ATCAGCTCCACGCATCAGCGACTACACATTCGACTCAGCAT CGACTACGCATCAGCTCCACGCATCAGCGACTACACATTCG ACTCAGCATCGACTACGCATCAGCTCCACGCATCAGCGACT ACACATTCGACTCAGCATCGACTACGCATCAGCTCCACGCA TCAGCGACTACACATTCGACTCAGCATCGACTACGCATCAG CTCCACGCATCAGCGACTACACATTCGACTCAGCATCGACT ACGCATCAGCTCCACGCATCAGCGACTACACATTCGACTCA GCATCGACTACGCATCAGCTCCACGCATCAGCGACTACACA TTCGACTCAGCATCGACTACGCATCAGCTCCACGCATCAGC GACTACACATTCGACTCAGCATGACTACACATTCGACTCAG CATCGACTACGCATCAGCTCCACGCATCAGCGACTACACAT TCGACTCAGCATCGACTACGCATCAGCTCCACGCATCAGCG ACTACACATTCGACTCAGCATCGACTACGCATCAGCTCCAC GCATCAGCGACTACACATTCGACTCAGCATCGACTACGCAT CAGCTCCACGCATCAGCGACTACACATTCGACTCAGCATCG ACTACGCATCAGCTCCACGCATCAGCGACTACACATTCGAC TCAGCATCGACTACGCATCAGCTCCACGCATCAGCGACTAC ACATTCGACTCAGCATCGACTACGCATCAGCTCCACGCATC AGCGACTACACATTCGACTCAGCATCGACTACGCATCAGCT CCACGCATCAGCGACTAAAAACTCGCGCCTACAGCGCATCA GCATACGACTACAACGACAGCAGCAGCAGCAGCAGCAGCAG CAGCGCCCCAGAAGAGAGAGAACACATTCGACTCAGCATCG ACTACGCATCAGCTCCACGCATTCAGCTCCACTACCGACGA TTAATCTACTACTACTCCCCTATTTCACCTATTTACATCAC AAAACCGACTCGACATCAGCTCTTCGCATCAGCTACGACGC ATCAAGCAGACGACTACGACCGCGCGACAGCAGCGACACTC CCGCGCAACCAACAGATAGATAGATAGAAAAACCGACTCGA CATCAGCTCTTCGCATCAGCTACGACGCATCAAGCAGACGA CTACGACCGCGCGACAGCAGCGACACTCCCGCGCAACCAAC AGATAGATAGATAGAAAAACCGACTCGACATCAGCTCTTCG CATCAGCTACGACGCATCAAGCAGACGACTACGACCGCGCG ACAGCAGCGACACTCCCGCGCAACCAACAGATAGATAGATA GAAAAACCGACTCGACATCAGCTCTTCGCATCAGCTACGAC GCATCAAGCAGACGACTACGACCGCGCGACAGCAGCGACAC TCCCGCGCAACCAACAGATAGATAGATAGAAAAACCGACTC GACATCAGCTCTTCGCATCAGCTACGACGCATCAAGCAGAC GACTACGACCGCGCGACAGCAGCGACACTCCCGCGCAACCA ACAGATAGATAGATAGAAAACCGACTCGACATCAGCTCTTC GCATCAGCTACGACGCATCAAGCAGACGACTACGACCGCGC GACAGCAGCGACACTCCCGCGCAACCAACAGATAGATAGAT AGAAAAACCGACTCGACATCAGCTCTTCGCATCAGCTACGA CGCATCAAGCAGACGACTACGACCGCGCGACAGCAGCGACA CTCCCGCGCAACCAACAGATAGATAGATAGAAAAACCGACT CGACATCAGCTCTTCGCATCAGCTACGACGCATCAAGCAGA CGACTACGACCGCGCGACAGCAGCGACACTCCCGCGCAACC AACAGATAGATAGATAGAAAAACCGACTCGCTACGACGCAT CAAGCAGACGACTACGACCGCGCGACAGCAGCGACACTCCC GCGCAACCAACAGATAGATAGATAGAAAAACCGACTCATCC GCCCCCCCCCCGCGCGCCGAACTAGACATCAGCTCTTCGCA TCAGCTACGACGCATCAAGCAGACGACTACGACCGCGCGAC AGCAGCGACACTCCCGCGCAACCAACAGATAGATAGATAGA
  36. 36. Genome Sequencing think big!!! The first bacterial genome (Haemophilus influenzae) The first eukaryotic genome (Saccharomyces cerevisiae) The first archaea genome (Methanococcus jannaschii) Homo), plants (Zea), and fungi (Coprinus) constitute small and peripheral branches of even eukaryotic cellular diversity. If the animals, plants, and fungi are taken to com- prise taxonomic “kingdoms,” then we must recognize as kingdoms at least a dozen other eucaryotic groups, all microbial, with as much or more independent evolutionary history than that which separates the three traditional eukaryotic kingdoms (13). The rRNA and other molecular data solidly confirm the notion stemming from the last century that the major organelles of eukaryotes—mitochondria and chloro- plasts—are derived from bacterial symbi- onts that have undergone specialization through coevolution with the host cell. Se- quence comparisons establish mitochondria as representatives of Proteobacteria (the group in Fig. 1 including Escherichia and Agrobacterium) and chloroplasts as derived from cyanobacteria (Synechococcus and Gloeobacter in Fig. 1) (14). Thus, all respi- ratory and photosynthetic capacity of eu- karyotic cells was obtained from bacterial symbionts; the “endosymbiont hypothesis” for the origin of organelles is no longer hypothesis but well-grounded fact. The nu- clear component of the modern eukaryotic cell did not derive from one of the pro- karoytic lineages, however. The rRNA and other molecular trees show that the eukary- otic nuclear line of descent extends as deep- ly into the history of life as do the bacterial and archaeal lineages. The mitochondrion and chloroplast came in relatively late. This late evolution is evidenced by the fact that mitochondria and chloroplasts diverged processing mechanisms occurred. Thus, modern representatives of Eucarya and Ar- chaea share many properties that differ from bacterial cells in fundamental ways. One ex- cleolar structural genes (12). W tutes a “nucleus?” Certainly the of the nuclear membrane was late event in the establishmen Fig. 1. Un genetic tre SSU rRNA Sixty-four quences r of all kno netic do aligned, an produced NAML (43, was modi in the co shown, by eages an branch po porate res analyses. T correspond changes p
  37. 37. The First Plant Genome Arabidopsis thaliana
  38. 38. $1000 per Genome in 2015 $1,000 $10,000 $100,000 $10 million US$100 million $1 million 2006 2008 2010 2012 2002 2004 As next-generation sequencers entered the market, the price dropped precipitously. The price of sequencing a whole human genome hovers around $5,000 and is expected to drop even lower. Cost of genome sequencing. Moore's law for computing costs. I n Silicon Valley, Moore’s law seems to stand on equal footing with the natural laws codified by Isaac Newton. Intel co-founder Gordon Moore’s iconic observation that computing power tends to double — and that its price there- fore halves — every 2 years has held true for nearly 50 years with only minor revision. But as an exemplar of rapid change, it is the target of playful abuse from genome researchers. In dozens of presentations over the past few years, scientists have compared the slope of Moore’s law with theswiftlydroppingcostsofDNAsequencing.Forawhile they kept pace, but since about 2007, it has not even been close. The price of sequencing an average human genome hasplummetedfromaboutUS$10milliontoafewthousand dollars in just six years. That does not just outpace Moore’s law— it makes theonce-powerfulpredictor of unbridled pro- gress look downright sedate. And just as the easy availability of personal computers changed the world, the breakneck pace of genome-technology development has revolutionized bioscience research. It is also set to cause seismic shifts in medicine. In the eyes of many, a fair share of the credit for this success goes toagrantschemerunbytheUSNationalHumanGenomeResearch Institute(NHGRI).OfficiallycalledtheAdvancedSequencingTech- nologyawards,itisknownmorewidelyasthe$1,000and$100,000 genome programmes. Started in 2004, the scheme has awarded grantsto97groupsofacademicandindustrialscientists,including some at every major sequencing company. Ithasencouragedmobilityandcooperationamongtechnologists, and helped to launch dozens of competing companies, staving off the stagnation that many feared would take hold after the Human GenomeProjectwrappedupin2003.“Themajorcompaniesinthe space have really changed the way people do sequencing, and it all startedwiththeNHGRIfunding,”saysGinaCosta,whohasworked forfiveinfluentialcompaniesandisnowavice-presidentatCypher Genomics, a genome-interpretation firm in San Diego, California. A GIANT’S LEGACY The $1,000 genome programme, now close to achieving its goal, will award its final grants this year. As technology enthusiasts look to future challenges, the coming milestone raises questions about how the roughly $230-million government programme managed to achieve such success, and whether its winning formula can be appliedelsewhere.Itbenefitedfromfortuitoustimingandthelackof anentrenchedindustry.ButJefferySchloss,directorofthedivision ofgenomesciencesattheNHGRIinBethesda,Maryland,whohas run the programme from its inception, says that its achievements alsosuggestthattherearewaystonavigatepublic–privatepartner- ships successfully. “One of our challenges is to figure out what is therightroleforthegovernment;tonotgetintheway,butfeedthe pipeline of private-sector technology development,” he says. The quest to sequence the first human genome was a massive BY ERIKA CHECK HAYDEN With a unique programme, the US government has managed to drive the cost of genome sequencing down towards a much-anticipated target. The$1,000 genome 2 9 4 | N A T U R E | V O L 5 0 7 | 2 0 M A R C H 2 0 1 4 © 2014 Macmillan Publishers Limited. All rights reserved modified from: Hayden EC. (2014) Nature 507:294–295.
  39. 39. Human Genome The human genome is 380,000 longer than the sequence shown here.
  40. 40. From Gene to Genome
  41. 41. Human Genome Project
  42. 42. Achievements beyond HGP
  43. 43. s et al. 2006). At that time, d bacterial genomes and only projects; this represented a from the mere two genomes er of sequenced genomes has ly in the last 10 years (Fig. 1), published. Today, there are more than 20,000 metagenomic projects publically available, and many terabytes of se- quencing data have been produced. The myriad of ecosys- tems includes numerous animal and human microbiomes, soils of all types, fresh and salt water samples, and even plant–microbe interaction systems. 0 2,000 4,000 6,000 8,000 10,000 12,000 14,000 16,000 Numberofgenomessequenced Year 20 Years of Bacterial Genome Sequencing Land M, et al. (2015) Funct Integr Genomics 15,141–161.
  44. 44. Deinococcus radiodurans Deinococcus radiodurans deinos—unusual extraordinarily resistant to oxidative stress, including desiccation and radiation survive under radiation around 3–5 million rad (100 rad can kill human)
  45. 45. genome 1 genome 2 genome 3 core genes decorative genes Comparative Genomics based on 16S sequences, DDH and biochemical tests some- times results in combinations or divisions that are not support- ed by their genome content. As a result, species, genera, and complete families are being shifted and reordered, in an ongo- ing process. dista 2013 Neg Acid quire of P Firm taxo the a deve for f Ozen New Micr ery eFig. 6 Core and pan-genome of 2085 E. coli genomes. Core gene decorative genes core genes
  46. 46. MicrobiomeWe are entering to the new era of omics, a wide variety of large-scale, multi-dimensional biology.
  47. 47. Features of Omics approach: high-throughput, data-driven, holistic, top-down methods understanding cell metabolism in one ‘integrated system’ high-output, requires bioinformatics to analyze & manipulate From Standalone Biology to ‘Omics’ Study
  48. 48. GENOMICS TRANSCRIPTOMICS PROTEOMICS METABOLOMICS DNA Metabolite Protein mRNA transcription metabolism translation Omics Study Relies on Central Dogma
  49. 49. Understand Genome is Not Enough genomics is static don’t know the set of genes that express in a particular condition some phenotypes are consequent of interaction of gene interaction (emerging property) lot of changes happen in the downstream processes of genetic information (not in DNA)
  50. 50. DNA Chip Microarray Chip
  51. 51. Microarray Technology
  52. 52. Microarray Data
  53. 53. Clustering of Microarray Data microarray data clustering tree on the top and left are just dendrogram always plots between genes versus conditions intensity of each color represents level of expression
  54. 54. 2D-gel Electrophoresis http://elte.prompt.hu/sites/default/files/tananyagok/practical_biochemistry/ch07s03.html
  55. 55. Comparative 2D-gel Electrophoresis http://elte.prompt.hu/sites/default/files/tananyagok/practical_biochemistry/ch07s03.html
  56. 56. modified from Venter et al. (2001) Science 291:1304–1351. pter 15 Genomics Transfer/carrier protein (203, 0.7%) Transcription factor (1850, 6.0%) Nucleic acid enzyme (2308, 7.5%) Signaling molecule (376, 1.2%) Receptor (1543, 5.0%) Kinase (868, 2.8%) Select regulatory molecule (988, 3.2%) Transferase (610, 2.0%) Synthase and synthetase (313, 1.0%) Oxidoreductase (656, 2.1%) Lyase (117, 0.4%) Ligase (56, 0.2%) Isomerase (163, 0.5%) Hydrolase (1227, 4.0%) Viral protein (100, 0.3%) Miscellaneous (1318, 4.3%) Cell adhesion (577, 1.9%) Chaperone (159, 0.5%) Cytoskeletal structural protein (876, 2.8%) Extracellular matrix (437, 1.4%) Immunoglobulin (264, 0.9%) Ion channel (406, 1.3%) Motor (376, 1.2%) Structural protein of muscle (296, 1.0%) Proto-oncogene (902, 2.9%) Select calcium-binding protein (34, 0.1%) Intracellular transporter (350, 1.1%) Transporter (533, 1.7%) Molecular function unknown (12,809, 41.7%) Signaltransduction Enzym e Nucleic acid binding None ᭿ FIGURE 15.10 Functional classification of the 26,383 genes predicted by Celera Genomics’ first draft of the sequence of the human genome. Each sector gives the number and percentage of gene products in each functional class in parentheses. Note that some classes overlap: a proto-oncogene, for example, may encode Not All Proteins Are Enzymes
  57. 57. Microbiome microbiome = all microbial population localize in a particular habitat (e.g.: human gut, skin, vagina, etc.)
  58. 58. Human Microbiome Studies
  59. 59. Hand–Skin Microbiome 51 college students (after exam) targeting V2 region of bacterial 16S rRNA gene >150 species/palm, intra- and interpersonal variation hand from the same individual share 17% of species-level phylotype women have higher diversity than men

×