The aim of this research project is to distinguish changes in gene expression, which are exclusively associated with age, from other general stress responses often caused by changes in nutrient availability based on microarray gene expression data of the model organism budding yeast (i.e. Saccharomyces Cerevisiae). The publically available dataset at NCBI titled "Time-course expression data during assurance of the chronological longevity by caloric restriction in budding yeast" with the accession number GSE41860 and access link http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41860 is one of the datasets that needs to be analyzed. Microarray data is provided in triplicates for any of the following 8 groups, which can be divided into 2 environmental conditions, i.e. caloric restriction (CR = i.e. 0.5% glucose) and YEPD (e.g. yeast extract peptone dextrose = 2% glucose) after 12, 18, 24 and 48 hours.
This is the first time I need to analyze time series data. Due to my severe visual impairment I need somebody, who can help me in selecting and then subsequently training me in using the most appropriate tools for achieving this objective.
The following 3 tools were recommended to me but I am open to other suggestions too, if you can convince me why those would be better than the once listed below:
1. Short Time-series Expression Miner (STEM) (see http://www.sb.cs.cmu.edu/stem/)
2. GenTχWarper (see http://www.psb.ugent.be/cbd/papers/gentxwarper/download.htm) and especially
3. The Gene Expression Dynamic Inspector (GEDI, see https://apps.childrenshospital.org/clinical/research/ingber/GEDI/download.htm).
I am looking for somebody, who can train me in the efficient usage of web interfaces, such as those 3 examples listed above, because due to my severe visual impairment I can only see a very small subsection of the screen. For my work on my bioinformatics PhD dissertation proposal I am depending on the usage of a screen-reader and magnification software named Zoomtext (see http://www.aisquared.com/products/) to access electronic information because I am legally blind. Hence, for example, if I need to use 8 times Zoomtext magnification, this software uses 64 pixels (8 pixels on the horizontal and 8 pixels on the vertical axis) to show on my screen what not visually impaired people see in a single pixel. Such kind of magnification allows me to read with my remaining very limited eyesight and to even use the mouse, but - because this high 8x magnification in the horizontal and vertical direction requires 64 times the space - my effective remaining visual field only consists of 1/64th of that of regular sighted people. This makes orientation on the screen very challenging. Therefore, in order to teach me how to use new web applications or software, my tutor/trainer needs to tell me exactly where on the screen I can find buttons, such as e.g. for uploading, submitting, visualizing, saving, analyzing, etc. data, so I know in which direction I need to scroll with my mouse so I can reach them. In the past, we have been using Team Viewer 5 and Skype to facilitate this training process because Team Viewer allows my tutor to view my screen from my perspective and hence he/she knows what I can see at any given time in order to determine which information I need next for performing the next steps of the analysis. Team Viewer (see http://www.teamviewer.com/en/) is a remote computer control software. Unfortunately, the only old version of Team Viewer, which works for this purpose, i.e. Team Viewer 5, is no longer available for download but I can email it to you if we'll work together. Because reading is extremely challenging and tiresome with my very limited remaining vision the best mode of communication is via Skype. My Skype ID is tfh002. Please feel free to send me a Skype invite any time if you have any thoughts about how I should proceed in overcoming the challenges described above even if you are not interested in working with me on this project long term. It took lots of external advice and brainstorming until I got to the point where I am today, i.e. making me able to identify the tools, for which I need to find a tutor next, and to communicate what kind of help I'd need to proceed to the next steps. That is why I am always open and very thankful for new ideas and inspirations.
I know that many portions of the analysis of time series data, such as the 3 tools listed above, can also be performed using the statistical software "R" or even other programs. If you'd prefer to use those instead of the above listed tools, I am open to it too. I have limited experiences using R Studio and I am happy to expand on them with your help.
Also, I need help to identify similar datasets to http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41860 because any conclusions derived from analyzing this particular dataset need to be validated on other similar datasets.
I am looking forward talking to you.