Hey guys. I am reading a great article (Ross, D. T.; Perou, C. M. Dis. Markers 2001, 17, 99–109), and am trying to figure out the genetic footprints and differences between 2 tumor cell lines. First I tried to manually compare colors in the original figure (http://genome-www.stanford.edu/breast_cancer/cell_line_review2001/images/figure1.html) and find red/green pairs, but something tells me there’s a more elegant way to use data. So I found supplementary sheets made by GenePix software (http://genome-www.stanford.edu/breast_cancer/cell_line_review2001/data/), for cell lines that I was interested in. These sheets got a bunch of columns with different names and values for every gene. Since I’m not familiar with gene expression lingo, could somebody point me to a column that shows the level of expression of a particular gene, ie the exact column that correlates to the color in the above linked picture?
Thanx!
Here are the columns:
SPOT
NAME
Clone ID
Gene Symbol
Gene Name
Cluster ID
Accession
Preferred name
CH1D_MEDIAN
CH1I_MEDIAN
CH1_PER_SAT
CH1I_SD
CH1B_MEAN
CH1B_MEDIAN
CH1B_SD
CH1D_MEAN
CH2I_MEAN
CH2D_MEAN
CH2D_MEDIAN
CH2I_MEDIAN
CH2_PER_SAT
CH2I_SD
CH2B_MEAN
CH2B_MEDIAN
CH2B_SD
CH2BN_MEDIAN
CH2DN_MEAN
CH2IN_MEAN
CH2DN_MEDIAN
CH2IN_MEDIAN
CORR
DIAMETER
FLAG
LOG_RAT2N_MEAN
LOG_RAT2N_MEDIAN
PIX_RAT2_MEAN
PIX_RAT2_MEDIAN
PERGTBCH1I_1SD
PERGTBCH1I_2SD
PERGTBCH2I_1SD
PERGTBCH2I_2SD
RAT1_MEAN
RAT1N_MEAN
RAT2_MEAN
RAT2_MEDIAN
RAT2_SD
RAT2N_MEAN
RAT2N_MEDIAN
REGR
SUM_MEAN
SUM_MEDIAN
TOT_BPIX
TOT_SPIX
X_COORD
Y_COORD
TOP
BOT
LEFT
RIGHT
SECTOR
SECTORROW
SECTORCOL
SOURCE
PLATE
PROW
PCOL
FAILED
IS_VERIFIED
IS_CONTAMINATED
LUID
Okay, I'm getting somewhere, and this (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM144001) helps. So, judging by the looks of the descriptions offered, I guess I need LOG_RAT2N_MEAN or RAT2N_MEAN.
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