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I understand this is not a biological question but this is often a problem whenever I look for literature.

How to look for a reference for some fact based on keywords. For instance you know about a fact such as - Cell signaling responses are faster but short lived compared to transcriptional responses. How to find the literature which actually says this. I often end up getting irrelevant results.

In other words, how to represent a fact using appropriate keywords. Is there an algorithm which can generate synonymous statements [like MeSH terms in pubmed] and search for those. Or is there any way of setting up a hierarchical search.

PS: If someone finds a reference for "Cell signaling responses are faster but short lived compared to transcriptional responses" then please let me know

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closed as too broad by WYSIWYG, Chris, Cornelius, anongoodnurse, Bez Dec 5 '14 at 0:02

There are either too many possible answers, or good answers would be too long for this format. Please add details to narrow the answer set or to isolate an issue that can be answered in a few paragraphs.If this question can be reworded to fit the rules in the help center, please edit the question.

You may want to have a look at Gene Ontology and at GOPubmed – nico Jun 18 '13 at 8:48
GO is about functional annotation of genes. That's not what I am looking for. GOPubmed is cool. I need to see if it has the function of search levels – WYSIWYG Jun 18 '13 at 8:50
perhaps set up a 'Google alert' with those phrases. – user3795 Jun 18 '13 at 11:26
I would either cite an advanced molecular biology or developmental biology textbook or if you must cite a paper, find the relevant chapter in the textbook and look at its references. – Drosophila Jun 18 '13 at 21:52

I think the statement above is slightly misleading. There are many many types of cell signalling, anything from RTK (at the cell surface or when its endocytosed), to steroid receptors, which operate on different time scales and produce different results depending on the type of signalling. Also it depends on what you are measuring/defining as a signal/response in lets say "cell signalling" because you could define cell signalling response as protein phosphorylation at any point in a signalling cascade or it could be the transcriptional activation itself (consider the MAPK pathway in Drosophila, at which point do you consider a response is produced? when Raf is activated? or when transcription factors such as pointed bind to their ETS binding site and start to transcribe as measured by luciferase? as you can tell the time difference between the two is quite large, well as far as I know after RTK activation in Drosophila it takes ERK 20 minutes just to translocate to the nucleus). A cell signalling response could also constitute changes in the rate of cell migration, cell shape etc, which can either be slow or fast depending on the signal in question. so I think the above question needs major rethinking and redefining.

Now getting back to your questions about key search terms, in my experience, over time you just end up developing a knack for what you consider to be key words after you carefully define the question and think bout its different aspects. A rule of thumb that I use is typing at name of proteins (e.g. JNK or RAS etc) or processes (transcription, phosphorylation etc) and use a word like rate, time-scale, half-life, turn-over or something like that if its measuring changes in time you are interested in. Just play around with words.

Also as a general advice you don't have to reference every snippet of every fact like "water is liquid at RT in standard atmospheric pressure" etc. References are meant to be there to acknowledge the work of others like "how DNA was discovered" so that people can't just lift paragraphs or pages out os someones research without acknowledging them and passing it as their own work.

Hope this helps.

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Thanks Bez. What I meant by fast and slow is the response time. Protein phosphorylations are much faster than transcriptional activation. Which I know for sure. Just wanted a review sort of thing which summarizes the response times of different processes in a cell. – WYSIWYG May 10 '14 at 6:26

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