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Questions tagged [metabolomics]

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Human metabolic pathways involving particular proteins

I am currently working on a project that involves analyzing the pathways in which certain proteins are involved. I have compiled a list of proteins, and I am keen to explore the pathways they ...
Shadan's user avatar
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1 vote
1 answer
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KEGG map01100: Is this ectomycorrhizae or arbuscular mycorrhizae

Just as background mycorrhizae are fungi and split into two groups ectomycorrhizae and arbuscular mycorrhizae (AM). Taxonomically these fungi groups are very distinct. Ectomycorrhizae belong to the ...
M__'s user avatar
  • 159
-4 votes
1 answer
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How to find out what biological effects a molecule has, without having a specific mechanism or pathway in mind?

I'm interested in finding what biological effects a (small) molecule has in a high-throughput and "low-assumption" way. I'm mainly interested in cell-based assays. Background: There are easy/...
Alex I's user avatar
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0 answers
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Is it possible to identify secreted metabolites or secondary metabolites from a gene list?

So I have a gene list obtained from differential gene expression analysis of a metabolic disease model, and I was wondering if I can identify metabolites or secondary metabolites that may be produced ...
Tasneem Qaqorh's user avatar
2 votes
1 answer
59 views

Can untargeted metabolomics detect epigenomic changes such as methylation?

My main focus is transcriptomics analysis and very recently I have also started working on metabolomics. From my transcriptomic data it looks like there is a gene/protein that could potentially ...
Sari's user avatar
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1 vote
0 answers
17 views

How many metabolites are in the metabolome of (almost) all eucaryotic cells?

Which small biomolecules (up to the size of amino acids) are present in (almost) every eucaryotic cell and thus part of its biochemical network, constantly and inevitably being produced and ...
Hans-Peter Stricker's user avatar
0 votes
1 answer
106 views

Proteomics data Vs Transcriptomics data?

I want to use either of Proteomics or Transcriptomics data for integrating it into my kinetic model. Before proceeding, I want to know what are the advantages of using either of them so that I could ...
iamakhilverma's user avatar
2 votes
1 answer
115 views

How to integrate transcriptomics data with kinetic metabolic models?

I have created a convenience kinetics† model. Now, I want to integrate the transcriptomics data with my convenience kinetics model for altering/weighing the kinetic parameter values. I have ...
iamakhilverma's user avatar
1 vote
1 answer
464 views

Can E. coli make pyruvate from acetate?

What pathway would E. coli use to make pyruvate from acetate? I have found several papers that refer to a possible mechanism that could move acetate to pyruvate via a three-step process: Step 1: ...
DWK's user avatar
  • 13
2 votes
1 answer
243 views

Normalizing Metabolomics data

First time posting. I recently started working in the field of metabolomics. I have semi-quantitative (not absolute concentration) LC-MS data from in-vitro cell experiments under different ...
Jon's user avatar
  • 21
0 votes
1 answer
97 views

Rate of production of enzymes in human [closed]

In the metabolic pathways, each of the reaction needs an enzyme(protein) in order to occur successfully. Is there any quantitative measure that can be associated to this enzyme? Like synthesis rate of ...
girl101's user avatar
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What does "each pathway define an independent genotype" mean?

In a section of this paper. However, if the question of independency is posed in the form: “Does each pathway shown define an independent genotype?,” then each of these three pathways is indeed ...
girl101's user avatar
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2 votes
1 answer
629 views

What is the meaning and significance of extreme pathways

Can someone please explain me what extreme pathways are? I found this definition in this article: Extreme pathways are a unique and minimal set of vectors that completely characterize the steady-...
girl101's user avatar
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0 votes
2 answers
116 views

Mathematical modelling of omics data [closed]

I'm interested in modelling host-pathogen interactions using mathematics. I know there are good resources in Pubmed but seems I'm looking for a book or introductory reviews. My background in maths is ...
biotech's user avatar
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1 vote
1 answer
155 views

Omics integration questions [closed]

Let's say that I have a population of Mus musculus in the lab. I divide it in a control group and a test group. The test group is constantly subjected to a stress (example: elevated UV radiation). ...
DGB's user avatar
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4 votes
1 answer
150 views

What makes alcohol harmful to mammals?

During the alcohol metabolic pathway, harmful by-products are made like acetaldehyde, hydroxyethyl, superox­ide anions, and hydroxyl radicals. How do these toxic compounds harm our tissues? Many of ...
James's user avatar
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