Bioinformatics – Functional Genomics – Dr. Víctor Treviño.

Presentación del tema: "Bioinformatics – Functional Genomics – Dr. Víctor Treviño."— Transcripción de la presentación:

1 Bioinformatics – Functional Genomics – Dr. Víctor Treviño

2  El metaboloma  Representa la colección de todos los metabolitos de un organismo biológico  Productos de función y expresión genética http://en.wikipedia.org/wiki/Metabolomics

3 SeparationDetection SampleSignal Gas chromatography (GC) High performance liquid chromatography (HPLC) Capillary electrophoresis (CE) Ultra-high pressure liquid chromatography (UPLC) Ion mobility Matrix-assisted laser desorption/ionization (MALDI) … Mass Spectrometry (mass-to-charge ratio) Fourier transform ion cyclotron resonance (FTMS) … NMR based detection Sample Signal nuclei spin resonance

4  NMR experiments is very quick  NMR equipment is quite expensive  MS is more sensitive than NMR  MS spectra can be wider than NMR

5 MS:m/z NMR:ppm [concentration] Visualization: 1 – Sample Example: TIC – Total Ion Counter

6  Los tiempos de retención de muchos metabolitos son conocidos  Otros se pueden aislar apartir del “pico” y luego estudiar para identificar

7 The Handbook of Metabonomics and Metabolomics (2007) – JeremyK. Nicholson, Elaine Holmes and John C. Lindon

8 Processing methods for differential analysis of LC-MS profile data - katajamaa - Oresic - BMC Bioinf 2005 Σ

9 MS:m/z NMR:ppm [concentration] Visualization: 1 – Sample Example: TIC – Total Ion Counter

10 MS:m/z NMR:ppm [concentration] Several Samples

11 Bins 0500150019601000 Samples BINS 

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13  Base line correction  Phasing / Alignment  Solvent Peak  NMR : TSP, … (3-trimethylsilylpropionic acid)  MS : Water  Standard  pH shifts  Temperature Effects

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16  Base-Line Subtraction  Suavizado  Moving Average  Used for smoothing  No data reduction  Overlapping windows  Binning  Used for smoothing…  … and data reduction  Non overlapping windows window size … … Integración

17  Phase Alignment  Scale

18 1. Corrección de línea base (remoción de background) 2. Suavizado (smoothing) 3. Binning (disminución de datos y suavizado) 4. Alineamiento de Picos 5. Normalización de Escala

19  Hierarchical Clustering (similar to Transcriptomics but using only sample clustering)  PCA – Principal Component Analysis -  Que software ya conocido podemos usar?  MeV

20 Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry - De Vos - Hall - Nat Prot 2007