In this directory you can download various data associated with the PlaNet database.
Description of the files:
-CelFileID.zip contains names of the cel files used to construct the PlaNet database.
-PlaNetStandalone.zip: Stand-alone version of PlaNet implemented in Python.
In addition, expression data, co-expression networks and HCCA obtained clusters are available under
archives termed by species names.
Each archive contains 4 files. For example, arabidopsis.zip contains:
1) "ExpMatAra step=3 rank=30.txt": this file describes association of genes to HCCA obtained clusters.
First column of the file contains gene number, while second column represents which cluster the
gene corresponds to. Gene number is corresponding to the line number found in *.EXP and *.HRR
file, i.e. number 0 corresponds to probeset AFFX-BioB-5_at. Remember that Python, as many
programming languages is 0-indexed!
2) “ExpMatAra.EXP”: this file contains normalized expression values used to calculate the HRRvalues. The first five columns of the file correspond to probeset ID, gene ID, description of the gene,
association to PFAM family and association to MapMan term, respectively. From sixth column on,
expression values start. Each row represents one probeset.
3) “ExpMatAra.HRR”: this file contains the HRR-value based co-expression network. The first five
columns are identical to the ones found in “ExpMatAra.EXP” file. From the sixth column, the file
contains information about the identity of probesets connected to the probeset represented by the
row of interest. For example, the first probeset in this file, AFFX-BioB-5_at, is connected 1+0, 2+1
and 26+2 (and others). This indicates that probeset AFFX-BioB-5_at is connected to probeset nr 2
with HRR=1 (remember that python is zero-indexed!). 2+1 means connected to probeset nr 3 with
HRR=2, and 26+2 means connected to probeset nr 27 with HRR=3.
4) “ExpMatAra.plt”: contains expression values used to generate ExpressionProfile plot for each gene.
In the first row of the file, description of the microarray is given. Expression values start from 2nd
row. The 1st column (from 2nd row on) contains the probeset ID. The 2nd column contains expression
values associated with a given description:
AFFX-r2-P1-cre-5_at
seedling - cotyledon 7d
4982-4529-4696-
In this example, expression values of probeset AFFX-r2-P1-cre-5_at on microarrays representing
“seedling - cotyledon 7d” are 4982,4529 and 4696.