I tried it since last 5 months and now going to complete it soon, but the problem is that i dont know how to get most important protein and how to discuss it in the discussion. I also dont know how and on what bases to pick the most important item of cellular component, molecular function, biological process and kegg pathways.
We don't know if OP has tried to talk/discuss the situation with the professor. @arjahejo has stated above that he comes from an underdeveloped country and is probably not used to the idea of learning as an interactive process. Unfortunately in most underdeveloped countries knowing more than your mentor is a considered a professional hazard so one gets used to doing things as asked, even if they don't make sense. Critical thinking/problem solving abilities (essential for a PhD) that students in developed countries get exposed to early in their undergraduate years are sadly absent most elsewhere.
@arjahejo: Tell us if you have given regular updates to your professor along the way. If you have not done this then it may be the reason why you find yourself to be in the situation you are in now. If you have been talking with the professor and are not receiving any guidance then you should seriously consider switching labs. PhD is a long term relationship and if you can't work with the mentor you will face bigger troubles down the road.
i am very near to it, please guide me further.
You haven't told us what you have done and the reasons behind those choices. What kind of an experiment was this that yielded the data you have. There may be no right answers for many scientific problems. Your success will be decided by the path you took, the results you got and a scientific explanation that you were able to formulate to fit those results/observations.
I must say that your professor sucks and you must report him (some universities allow this). Your mentor should be a "mentor", explain to you what is the purpose of the analysis, what is the biological context and if he/she is not capable to teach you the necessary skills, to support you with classes/courses/workshops.
Relate to your question, a Gene Ontology (Enrichment) analysis simply reports if a group of genes belongs to some particular categories based on statistics like "what is the probability of having 10 genes belonging to the same GO class based on a test group". Tools like AmiGO or DAVID, Panther, GOrilla, etc. can do the test, simply use your list of genes as input and select categories by a P-value threshold keeping classes that are statistically overrepresented in your sets. But the question about what is important in biological terms it is only answered knowing the experiment, what are the conditions? which metabolic pathways are expected to be modified? why 40hr? etc.
I was also going to mention DAVID: https://david.ncifcrf.gov/summary.jsp
You could start there, input your list of genes from each part of the analysis as separate lists, select Functional Annotation Clustering, and focus on Gene Ontology terms (the defaults are already selected) to start. This will produce terms with Benjamini Hochberg P values, I believe.
Ultimately, being a researcher is about taking control of a project and forming your own hypotheses and conclusions based on what your data is saying to you. Guidance is needed of course.
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maybe you should consider a different profession?
The man who comes from undeveloped country to developed one for PhD, don't know about recent tools, techniques used in research. In the beginning assigned very difficult task, to write a paper from a research which done by another person. But i accept this task i am very near to it, please guide me further.
Given the information you provided, I'm not entirely clear how to help you. I'm not sure how to make gene ontology enrichment analysis suck less for you.
Could you please tell me one thing that, how to pick the most important cellular component ? What are the rules to pick it?
For example 1-cytoplasm- Observed 30 proteins. 2-intracellular part-Observed 23 proteins. 3-intracellular-Observed 20 proteins.
There is no such thing as 'most important'. Everything inside and outside the cell is important, it just depends what your question is.
That 1 protein in the cytoplasm might be responsible for lots of effects, if it's a transcriptional regulator for example, but it is just as important as the 30 proteins it might control, that actually have a phenotypic effect.
Sounds like you're too focused on the number of proteins that seem to be enriched, rather than what they do, and whether them being enriched in your test conditions makes any biological sense.
You will need to give a lot more information on your research questions and the analysis you performed, because giving advice in this setting is rather hard.