Understanding the expression table
Making sense of the columns in the gene expression tableTranscript: Overlapping 46 bp Solexa sequences were assembled into contigs (short for contiguous) and assigned a number. The 'ctg' tells you you're looking at a contig. The 'code' switches in some tables, so if you see a 'cf' id number, just think contig.
1N_Rn 1Nm 1No 1Np 1Rj 1Rk 1Rl 1Sa 1Sb 1Sc 1Sd 1Se 1Sf 1Sg 2Sh 3Si: Each of these columns tells you how many different copies of the specific contig were present in the RNA isolated from plants at the specified developmental stage. To understand what these developmental stages are, be sure to click on the "shoot, root, nodule" link on the "Gene expression" strategy page. Here are a few things to remember. The 1 indicates that RNA was isolated from plants from MN, 2 is from KS, and 3 is from OK. If you are doing a developmental comparision, you will want to use just the columns labeled with a 1. N stands for nodule, R for root, and S for shoot. The lower case letters tell you about the age of the plant when the specific tissue was removed for RNA isolation. You might also find the vertical line separating the below ground (R and N) and above ground (S) sample to be helpful. If you are interested in shoot development, you might want to focus on samples to the right of the vertical line (but only until you get to 2 for KS).
sumRnormd and sumSnormd: Total root and shoot expression is summed and normallized in these two columns. This is not going to be particularly helpful information for most of the questions you'll be asking.
fold chg:Comparison of root and shoot expression levels. This compares the previous two columns and isn't particularly informative.
flwry:Just a nomenclature to group transcripts. Not so useful.
At gene:Helpful column that maps Arabidopsis thaliana(At) genes to the contigs. The space below a gene symbol means that several contigs map to the same Arabidopsisgene.
PTHR/Uref90: These are "Panther" gene names assigned to the contigs by a software program. Panther looks for recognizable sequence domains and predicts what family of genes a sequence likely belongs to. This is a great place to start if you are looking for genes with particular functions.
NOTE:The other two expression tables have the expression information for over 40,000 contigs. This table is just for the contigs that map to the shoot candidate genes. If you're interested in overall gene expression patterns, you'll want to tackle the larger data sets. Open them in Excel 2008 so all the data can be seen.
1N_Rn 1Nm 1No 1Np 1Rj 1Rk 1Rl 1Sa 1Sb 1Sc 1Sd 1Se 1Sf 1Sg 2Sh 3Si: Each of these columns tells you how many different copies of the specific contig were present in the RNA isolated from plants at the specified developmental stage. To understand what these developmental stages are, be sure to click on the "shoot, root, nodule" link on the "Gene expression" strategy page. Here are a few things to remember. The 1 indicates that RNA was isolated from plants from MN, 2 is from KS, and 3 is from OK. If you are doing a developmental comparision, you will want to use just the columns labeled with a 1. N stands for nodule, R for root, and S for shoot. The lower case letters tell you about the age of the plant when the specific tissue was removed for RNA isolation. You might also find the vertical line separating the below ground (R and N) and above ground (S) sample to be helpful. If you are interested in shoot development, you might want to focus on samples to the right of the vertical line (but only until you get to 2 for KS).
sumRnormd and sumSnormd: Total root and shoot expression is summed and normallized in these two columns. This is not going to be particularly helpful information for most of the questions you'll be asking.
fold chg:Comparison of root and shoot expression levels. This compares the previous two columns and isn't particularly informative.
flwry:Just a nomenclature to group transcripts. Not so useful.
At gene:Helpful column that maps Arabidopsis thaliana(At) genes to the contigs. The space below a gene symbol means that several contigs map to the same Arabidopsisgene.
PTHR/Uref90: These are "Panther" gene names assigned to the contigs by a software program. Panther looks for recognizable sequence domains and predicts what family of genes a sequence likely belongs to. This is a great place to start if you are looking for genes with particular functions.
NOTE:The other two expression tables have the expression information for over 40,000 contigs. This table is just for the contigs that map to the shoot candidate genes. If you're interested in overall gene expression patterns, you'll want to tackle the larger data sets. Open them in Excel 2008 so all the data can be seen.
