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Questions tagged [pathway]

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Role of Snail 1 and ZEB 1 in Notch pathway in case of breast cancer?

Currently I am working on Notch pathway in breast cancer and want to know that how can we target the protein of this pathway by some natural phytochemicals? Also, is there any role of snail 1 and ...
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60 views

What determines the metabolic pathways that a biological cell is able to carry?

For example: human cells (eukaryotes) can utilize the Kreb's cycle pathway to generate more ATP after glycolysis, but most bacteria cannot utilise the Kreb's cycle plant cells can utilise the ...
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1answer
24 views

Query regarding KEGG KGML pathway files

With respect to the the Wnt pathway in KEGG, the KGML file of this pathway has description of each interaction between a pair of genes. These interactions are designated in the form: ...
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Simplest known form of aerobic glycolysis

What is the simplest known way that an organism performs aerobic glycolysis? In other words, what is the simplest known way known to convert glucose into $\ce{H2O}$ and $\ce{CO2}$, other than by ...
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Producing 1,2 propanediol in engineered organism

So we have the following pathways in a engineered organism to produce 1,2 propanediol: So I don't understand why wouldn't we knock out the acetic acid since it is a sideproduct. Only reason I could ...
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83 views

How to surpass cell death?

Is it possible to surpass/decay cell death. For example to disable the process muscles cells death, by tweaking the transduction pathways: If it's not possible in our age Medicine, what it would ...
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1answer
4k views

Regulation of Glycolysis and other pathways at ‘irreversible’ reaction steps

The hexokinase, phosphofructokinase and pyruvate kinase steps of glycolysis (1,3 and 10, below) are the only ones that are irreversible, and are also the steps where glycolysis is regulated. Is it ...
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65 views

Why Differential equation is not a good way to model chemical reaction networks [closed]

I'm a computer scientist and mostly code and have worked with Boolean models of cell level molecule transfer. Now i'm reading about the Biological pathways and modelling chemical reaction networks / ...
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1answer
25 views

What are some online databases that I can search to find the pathways for sythesis of Lignin, Cellulose, GAX?

I am trying to obtain the pathway information for synthesis of Lignin,GAX and Cellulose in Sorghum. I am quite new to biology and genetics (EE background). I would appreciate it if y'all can provide ...
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1answer
865 views

Exact definition of 'convergent' and 'divergence' in cell signalling?

From what I understand, we refer to 'signal convergence' as being when two different ligands/stimuli lead to the same (at least in part) responses inside a single cell. This may or may not be due to ...
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1answer
454 views

How is the rate of gluconeogenesis controlled in the cell?

As far as I am aware, all steps in glycolysis are readily reversible except the phosphorylation of glucose, the phosphorylation of fructose6 phosphate, and the phosphorylation of phosphoenolpyruvate ...
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1answer
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Organism-specific Kegg Pathway: Must all boxes be high-lighted/present for a reaction to occur?

I'm new to using Kegg and not sure how to interpret the position of the pathway enzymes in the pathway that I'm looking at. More specifically: If all boxes (of KOs) must be present/colored green or ...
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Why is the hexose monophosphate shunt called a direct oxidative pathway?

Why is the hexose monophosphate shunt (pentose phosphate pathway) called a direct oxidative pathway( Ref. Biochemistry by Satyanarayana , 4th edition, pg.no: 244) , even though oxygen molecule is not ...
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3answers
74 views

How do I score differential activity of cellular pathways in microarray data (not enrichment)?

I would like to identify cellular pathways (KEGG) with discriminative changes in the average activity (expression levels) of their gene members in a two-condition microarray dataset. The goal is to ...
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1answer
80 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 ...
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What would the presence of a hub metabolite in a metabolic pathway signify?

Say I have a metabolic pathway, consisting of multiple metabolites and reactions. On analyzing the pathway I find that among all the metabolite, one metabolite is the hub metabolite (hub metabolite is ...
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1answer
31 views

differentially expressed genes of the treated with estradiol samples

I did differential analysis on samples treated (G1E-ER4) with estradiol (differentiation induced by estradiol) and control (G1E). The genes that I gor as differentially expressed in G1E-ER4 showed ...
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438 views

If so many different hormones/molecules work by activating adenylyl cyclase, how do they have different effects?

It seems that many hormones and molecules work by activating adenylyl cyclase to convert $\text{ATP}$ to $\text{cAMP}$, such as adrenaline and glucagon. Both of these seem to bind to $\text G$ protein ...
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1answer
203 views

What is the molecular mechanism of odorant transduction signaling pathway?

I have read a few papers on the topic of odorant signaling pathway. The following papers are listed as examples. However, I found that there is not a clear pathway representation of the odorant ...
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If two different diseases have more than one common pathway, the relationship between their occurences?

I just wonder that are there any special relationship between the pathway and disease occurrence. For example, there are cancer A and cancer B (and they have more than one common pathway). Then if ...
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1answer
51 views

Finding a reaction from a KEGG map

I have come across a map and a part of it looks like this: Now I have not been able to locate the reaction that converts alpha D-Glucose to Glucono-1,5-lactone but was successfully able to locate ...
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1answer
115 views

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 ...
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1answer
288 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-...
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1answer
8k views

GPCRs: Gi and Gs

GPCR = G-protein coupled receptor Gi = G inhibitory alpha subunit Gs = G stimulatory alpha subunit Are there structural differences between Gi and Gs subunits (secondary structure)? Or is it just ...
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1answer
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Do non-enzyme catalysed reaction pathways exist?

Can their be a kind of chemical reaction pathway in a cell, that is catalyzed or regulated but NOT necessarily by enzymes? I could not find anything on Google. I have almost no background in biology, ...
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2answers
302 views

Difficulties understanding a pathway [closed]

I am not a biologist and I would love to understand what is going on with this pathway. I went to the description but it's still complicated, and I couldn't follow. Can someone please help me with it? ...
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Which data format for mRNA expression matrix is necessary to run pathway analysis with Paradigm?

I am running Paradigm on a matrix of mRNA expression. I read Vaske, Charles J., et al. "Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM."...