Honestly, the past months have been overwhelm for me.
My professor in this first world country universty task me with a simple question for me to complete my PhD (due in 5 month).
"Look online for gene 'A' pathway network and come back with expression pattern of its associated genes in different type of diseases cells to identify important(hub?) proteins so we can compare with our lab mutated cell results and treatment"
And now I am totally lost how to start and what to do to proceed.
I only graduate from third world country university with minimal computational biology training. Im taking online R programming course now (I read you need to use BioConductor to analyse NGS data) but that seem to be steep learning curve for me (no worries, still climbing that hill and not going to give up yet). I read you need to use Cytoscape so you can use NGS data to make pathway. But how to download and filter and compare? And most tutorial on GSEA (this is for filtering the NGS data right?) seem to imply readers know where to get the initial inout data. And finally, what to "click" to download from NCBI Geo and what next after that?
If only somebody outhere willing to talk/guide me I will be very appreciate. Sorry for rambling.
Sincerely, Lost Soul