{"id":332,"date":"2018-06-15T16:27:16","date_gmt":"2018-06-15T23:27:16","guid":{"rendered":"http:\/\/blogs.reed.edu\/compbio\/?p=332"},"modified":"2018-06-15T16:27:16","modified_gmt":"2018-06-15T23:27:16","slug":"week-4-obtaining-and-processing-data","status":"publish","type":"post","link":"https:\/\/blogs.reed.edu\/compbio\/2018\/06\/15\/week-4-obtaining-and-processing-data\/","title":{"rendered":"Week 4: Obtaining and Processing Data"},"content":{"rendered":"

This week our main goal has been to find a pipeline to obtain TCGA data in a neat form. We discovered UCSC’s Xena Browser,<\/a> which has files from the TCGA and a number of other databases.<\/p>\n

Last week, we used the data from FireBrowse to make a graph of the genes that have patients with abnormally high or low levels of expression.<\/p>\n

\"\"
Number of patients that have abnormally high or low levels of expression<\/figcaption><\/figure>\n

This week we changed that graph slightly by showing the difference between the number of patients with high expression and the number of patients with low expression by gene.<\/p>\n

\"\"
Number of patients by gene that have abnormally high or abnormally low levels of gene expression.<\/figcaption><\/figure>\n

It is interesting to me that there are generally more patients with severe under-expression rather than severe-overexpression. I wonder if this is because these genes play a role in suppressing tumors, and that therefore maybe under-expression is more likely to cause cancer than overexpression?<\/p>\n

I also worked on integrating gene expression data from Xena into our graph of the Wnt pathway.<\/p>\n

\"\"
Wnt Pathway from PathLinker with Gene Expression Data. Red = high, orange = medium-high, yellow= medium, green = low, blue(not shown) = very low, white(not shown) = no expression. Triangles are transcription factors, squares are receptors, circles are intermediate proteins.<\/figcaption><\/figure>\n

Kathy figured out what was wrong with PathLinker the first time we ran it and re-ran it. I am working on turning it into a graph, but the input data is very different because it’s coming from a different version of NetPath so I need to change the program to be able to process the new data.<\/p>\n

I also noticed while I was processing the expression data from Xena that there was a large amount of variability in gene expression between patients. I’m currently working on several things. Instead of just averaging gene expression for genes I’m comparing gene expression patient-by-patient so I’m comparing a tumor sample to a normal tissue sample for every patient. I also want to come up with a way to visualize the variance of expression among patients, because the more variance there is the less significant differences in expression between cancerous and normal tissue are. Anna suggested I do this by making the borders on nodes with high variance thicker. I am also going back and checking my math on gene expression to make sure that it is actually statistically significant and is conducted in a way that is similar to how other researchers have done similar research in the past.<\/p>\n","protected":false},"excerpt":{"rendered":"

This week our main goal has been to find a pipeline to obtain TCGA data in a neat form. We discovered UCSC’s Xena Browser, which has files from the TCGA and a number of other databases. Last week, we used the data from FireBrowse to make a graph of the genes that have patients with … Continue reading “Week 4: Obtaining and Processing Data”<\/span><\/a><\/p>\n","protected":false},"author":1800,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4,9,11,1],"tags":[],"class_list":["post-332","post","type-post","status-publish","format-standard","hentry","category-biology","category-cancer","category-summer-research-2018","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/posts\/332","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/users\/1800"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/comments?post=332"}],"version-history":[{"count":8,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/posts\/332\/revisions"}],"predecessor-version":[{"id":345,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/posts\/332\/revisions\/345"}],"wp:attachment":[{"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/media?parent=332"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/categories?post=332"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/tags?post=332"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}