Metabolomics - Revision history

Zhennan at 02:02, 28 June 2016

2016-06-28T02:02:25Z

Zhennan at 10:24, 27 June 2016

2016-06-27T10:24:36Z

Xysj1990: /* What is Metabolomics ? */

2016-06-21T15:46:15Z

‎What is Metabolomics ?

Xysj1990: /* What is Metabolomics ? */

2016-06-21T15:46:07Z

‎What is Metabolomics ?

Rice2012: /* Projects List */

2016-06-21T07:28:22Z

‎Projects List

Rice2012: /* What is Metabolomics ? */

2016-06-21T07:27:44Z

‎What is Metabolomics ?

Rice2012: /* What is Metabolomics ? */

2016-06-21T07:27:35Z

‎What is Metabolomics ?

Rice2012: Created page with "==What is Metabolomics ?== * Metabolomics is the scientific study of chemical processes involving metabolites. Specifically, metabolomics is the "systematic study of the uniqu..."

2016-06-21T07:27:20Z

Created page with "==What is Metabolomics ?== * Metabolomics is the scientific study of chemical processes involving metabolites. Specifically, metabolomics is the "systematic study of the uniqu..."

New page

==What is Metabolomics ?==
* Metabolomics is the scientific study of chemical processes involving metabolites. Specifically, metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite profiles.<ref name="ref1"/> The metabolome represents the collection of all metabolites in a biological cell, tissue, organ or organism, which are the end products of cellular processes.[2] mRNA gene expression data and proteomic analyses reveal the set of gene products being produced in the cell, data that represents one aspect of cellular function. Conversely, metabolic profiling can give an instantaneous snapshot of the physiology of that cell. One of the challenges of systems biology and functional genomics is to integrate proteomic, transcriptomic, and metabolomic information to provide a better understanding of cellular biology.
[[File: IC4R-Metabolomics-overview-1.png|center|thumb|970px|'''Figure 1. Integrated functional genomics. The effects of gene perturbations are evaluated at multiple levels including the transcriptome, proteome, and metabolome. Changes in the metabolome occur as a consequence of those changes in the transcriptome that result in changes in the levels or catalytic activities of enzymes. Therefore, metabolome analysis is a valuable tool for inferring gene function.''']]
* Advances in mass spectrometry have enabled the analysis of cellular proteins and metabolites (proteome and metabolome respectively) on a scale previously unimaginable. The cumulative utilization of these technologies has advanced the fields of functional genomics (Holtorf et al., 2002; Oliver et al., 2002; Somerville and Somerville, 1999) and systems biology (Ideker et al., 2001; Kitano, 2000). Both fields comprise traditional molecular biology, enzymology and bio- chemistry; however, the predominant difference from previous approaches is the significantly larger scale upon which they are conducted.
==Limitations of metabolomics ==
* The major limitation of metabolomics is its current inability to comprehensively profile all of the metabolome. This inability is directly related to the chemical complexity of the metabolome, the biological variance inherent in most living organisms, and the dynamic range limitations of most instrumental approaches. In many ways, this is similar to the situation of the Human Genome Project in 1990, when the technological means to sequence genomes were not yet available.
==Metabolome technologies==
* It is generally accepted that a single analytical technique will not provide sufficient visualization of the metabolome and, therefore, multiple technologies are needed for a comprehensive view (Hall et al., 2002; Sumner et al., 2002). Accordingly, many analytical technologies have been enlisted to profile the metabolome. Methods based on infrared spectroscopy (IR) (Oliver et al., 1998), nuclear magnetic resonance (NMR(Bligny and Douce, 2001; Ratcliffe and Shachar-Hill,2001; Roberts, 2000), thin layer chromatography (TLC) (Tweeddale et al., 1998), HPLC with ultraviolet and photodiode array detection (LC/UV/PDA) (Fraser et al., 2000), capillary electrophoresis coupled to ultravio- let absorbance detection (CE/UV) (Baggett et al., 2002), capillary electrophoresis coupled to laser induced fluorescence detection (CE/LIF) (Arlt et al., 2001), capillary electrophoresis coupled to mass spectrometry (CE/MS) (Soga et al., 2002), gas chromatography-mass spectrometry (GC/MS), liquid chromatography-mass spectro- metry (LC/MS) (Huhman and Sumner, 2002), liquid chromatography tandem mass spectrometry (LC/MS/ MS) (Huhman and Sumner, 2002), Fourier transform ion cyclotron mass spectrometry (FTMS) (Aharoni et al., 2002), HPLC coupled with both mass spectrometry and nuclear magnetic resonance detection (LC/NMR/ MS) (Bailey et al., 2000a), and LC/NMR/MS/MS (Bai- ley et al., 2000b) have all been used.
==Projects List==

{|class="wikitable sortable" style="width:100%;text-align:center"
|-
!Project Title
!Species
!Published years
!Academic Journal
!RiceWiki Project ID
|-
|'''Genetic analysis of the metabolome exemplified using a rice population'''
|''Oryza sativa''
|2013
|Proceedings of the National Academy of Sciences
|[[IC4R001-Metabolomics-2013-24259710]]
|-
|'''Folate fortification of rice by metabolic engineering'''
|''Oryza sativa L. ssp. Japnoica''
|2007
|Nature Biotechnology
|[[IC4R002-Metabolomics-2007-17934451]]
|-
|'''Characterization of Volatile Aroma Compounds in Cooked Black Rice'''
|''Oryza sativa''
|2007
|Journal of Agricultural and Food Chemistry
|[[IC4R003-Metabolomics-2007-18081248]]
|-
|'''A targeted metabolomics approach toward understanding metabolic variations in rice under pesticide stress'''
|''Oryza sativa''
|2015
|Analytical Biochemistry
|[[IC4R004-Metabolomics-2015-25766578]]
|-
|'''Metabolomic screening applied to rice FOX Arabidopsis lines leads to the identification of a gene-changing nitrogen metabolism.'''
|''Oryza sativa L. ssp. japonica''
|2010
|Molecular Plant
|[[IC4R005-Metabolomics-2010-20085895]]
|-
|'''Application of a metabolomic method combining one-dimensional and two-dimensional gas chromatography-time-of-flight/mass spectrometry to metabolic phenotyping of natural variants in rice'''
|''Oryza sativa L.''
|2007
|Journal of Chromatography B
|[[IC4R006-Metabolomics-2007-17556050]]
|-
|'''Metabolic profiling of transgenic rice with cryIAc and sck genes: An evaluation of unintended effects at metabolic level by using GC-FID and GC–MS'''
|''Oryza sativa L.''
|2009
|Journal of Chromatography B
|[[IC4R007-Metabolomics-2009-19233746]]
|}
==References==
<references>
<ref name="ref1">
https://en.wikipedia.org/wiki/Epigenome
</ref>
</references>

@@ Line 75: / Line 75: @@
 |''Oryza sativa''
 |2015
-|Mol Plant
+|Plant Molecular Biology Reporter
 |'''[[IC4R010-Metabolomics-2015-25578272]]'''
 |-
@@ Line 81: / Line 81: @@
 |''Oryza sativa''
 |2015
-|Plant J
+|Plant Journal
 |'''[[IC4R011-Metabolomics-2015-25267402]]'''
 |-
@@ Line 87: / Line 87: @@
 |''Oryza sativa''
 |2012
-|Plant J
+|Plant Journal
 |'''[[IC4R012-Metabolomics-2012-22229385]]'''
 |}

@@ Line 59: / Line 59: @@
 |Journal of Chromatography B
 |'''[[IC4R007-Metabolomics-2009-19233746]]'''
 |}

@@ Line 1: / Line 1: @@
 ==What is Metabolomics ?==
 * Metabolomics is the scientific study of chemical processes involving metabolites. Specifically, metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite profiles.<ref name="ref1"/> The metabolome represents the collection of all metabolites in a biological cell, tissue, organ or organism, which are the end products of cellular processes.[2] mRNA gene expression data and proteomic analyses reveal the set of gene products being produced in the cell, data that represents one aspect of cellular function. Conversely, metabolic profiling can give an instantaneous snapshot of the physiology of that cell. One of the challenges of systems biology and functional genomics is to integrate proteomic, transcriptomic, and metabolomic information to provide a better understanding of cellular biology.<br><br>
-[[File: IC4R-Metabolomics-overview-1.png|center|thumb|970px|'''Figure 1. Integrated functional genomics. The effects of gene perturbations are evaluated at multiple levels including the transcriptome, proteome, and metabolome. Changes in the metabolome occur as a consequence of those changes in the transcriptome that result in changes in the levels or catalytic activities of enzymes. Therefore, metabolome analysis is a valuable tool for inferring gene function.''']]<br><br>
+[[File: IC4R-Metabolomics-overview-1.png|center|thumb|970px|'''Figure 1. Integrated functional genomics. The effects of gene perturbations are evaluated at multiple levels including the transcriptome, proteome, and metabolome. Changes in the metabolome occur as a consequence of those changes in the transcriptome that result in changes in the levels or catalytic activities of enzymes. Therefore, metabolome analysis is a valuable tool for inferring gene function.''']]<br>
 * Advances in mass spectrometry have enabled the analysis of cellular proteins and metabolites (proteome and metabolome respectively) on a scale previously unimaginable. The cumulative utilization of these technologies has advanced the fields of functional genomics (Holtorf et al., 2002; Oliver et al., 2002; Somerville and Somerville, 1999) and systems biology (Ideker et al., 2001; Kitano, 2000). Both fields comprise traditional molecular biology, enzymology and bio- chemistry; however, the predominant difference from previous approaches is the significantly larger scale upon which they are conducted.

@@ Line 22: / Line 22: @@
 |2013
 |Proceedings of the National Academy of Sciences
-|[[IC4R001-Metabolomics-2013-24259710]]
+|'''[[IC4R001-Metabolomics-2013-24259710]]'''
 |-
 |'''Folate fortification of rice by metabolic engineering'''
@@ Line 28: / Line 28: @@
 |2007
 |Nature Biotechnology
-|[[IC4R002-Metabolomics-2007-17934451]]
+|'''[[IC4R002-Metabolomics-2007-17934451]]'''
 |-
 |'''Characterization of Volatile Aroma Compounds in Cooked Black Rice'''
@@ Line 34: / Line 34: @@
 |2007
 |Journal of Agricultural and Food Chemistry
-|[[IC4R003-Metabolomics-2007-18081248]]
+|'''[[IC4R003-Metabolomics-2007-18081248]]'''
 |-
 |'''A targeted metabolomics approach toward understanding metabolic variations in rice under pesticide stress'''
@@ Line 40: / Line 40: @@
 |2015
 |Analytical Biochemistry
-|[[IC4R004-Metabolomics-2015-25766578]]
+|'''[[IC4R004-Metabolomics-2015-25766578]]'''
 |-
 |'''Metabolomic screening applied to rice FOX Arabidopsis lines leads to the identification of a gene-changing nitrogen metabolism.'''
@@ Line 46: / Line 46: @@
 |2010
 |Molecular Plant
-|[[IC4R005-Metabolomics-2010-20085895]]
+|'''[[IC4R005-Metabolomics-2010-20085895]]'''
 |-
 |'''Application of a metabolomic method combining one-dimensional and two-dimensional gas chromatography-time-of-flight/mass spectrometry to metabolic phenotyping of natural variants in rice'''
@@ Line 52: / Line 52: @@
 |2007
 |Journal of Chromatography B
-|[[IC4R006-Metabolomics-2007-17556050]]
+|'''[[IC4R006-Metabolomics-2007-17556050]]'''
 |-
 |'''Metabolic profiling of transgenic rice with cryIAc and sck genes: An evaluation of unintended effects at metabolic level by using GC-FID and GC–MS'''
@@ Line 58: / Line 58: @@
 |2009
 |Journal of Chromatography B
-|[[IC4R007-Metabolomics-2009-19233746]]
+|'''[[IC4R007-Metabolomics-2009-19233746]]'''
 |}
 ==References==
 <references>

@@ Line 2: / Line 2: @@
 * Metabolomics is the scientific study of chemical processes involving metabolites. Specifically, metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite profiles.<ref name="ref1"/> The metabolome represents the collection of all metabolites in a biological cell, tissue, organ or organism, which are the end products of cellular processes.[2] mRNA gene expression data and proteomic analyses reveal the set of gene products being produced in the cell, data that represents one aspect of cellular function. Conversely, metabolic profiling can give an instantaneous snapshot of the physiology of that cell. One of the challenges of systems biology and functional genomics is to integrate proteomic, transcriptomic, and metabolomic information to provide a better understanding of cellular biology.
 [[File: IC4R-Metabolomics-overview-1.png|center|thumb|970px|'''Figure 1. Integrated functional genomics. The effects of gene perturbations are evaluated at multiple levels including the transcriptome, proteome, and metabolome. Changes in the metabolome occur as a consequence of those changes in the transcriptome that result in changes in the levels or catalytic activities of enzymes. Therefore, metabolome analysis is a valuable tool for inferring gene function.''']]
-* Advances in mass spectrometry have enabled the analysis of cellular proteins and metabolites (proteome and metabolome respectively) on a scale previously unimaginable. The cumulative utilization of these technologies has advanced the fields of functional genomics (Holtorf et al., 2002; Oliver et al., 2002; Somerville and Somerville, 1999) and systems biology (Ideker et al., 2001; Kitano, 2000). Both fields comprise traditional molecular biology, enzymology and bio- chemistry; however, the predominant difference from previous approaches is the significantly larger scale upon which they are conducted.
+* Advances in mass spectrometry have enabled the analysis of cellular proteins and metabolites (proteome and metabolome respectively) on a scale previously unimaginable. The cumulative utilization of these technologies has advanced the fields of functional genomics (Holtorf et al., 2002; Oliver et al., 2002; Somerville and Somerville, 1999) and systems biology (Ideker et al., 2001; Kitano, 2000). Both fields comprise traditional molecular biology, enzymology and bio- chemistry; however, the predominant difference from previous approaches is the significantly larger scale upon which they are conducted.<br><br>
 ==Limitations of metabolomics ==
 * The major limitation of metabolomics is its current inability to comprehensively profile all of the metabolome. This inability is directly related to the chemical complexity of the metabolome, the biological variance inherent in most living organisms, and the dynamic range limitations of most instrumental approaches. In many ways, this is similar to the situation of the Human Genome Project in 1990, when the technological means to sequence genomes were not yet available.