Adding expression data
Expression data should be processed using LSTrAP, this will generate the expression matrix, coexpression networks and clusters that can be directly imported into CoNekt. Note that in some cases additional files, containing meta information, need to be provided.
Adding expression profiles
In the 'Admin panel', under 'Add' -> 'Expression profiles'. Select the species and the source (currently only LSTrAP expression matrices are supported).
Next, select the expression matrix (generated using LSTrAP). Using a normalized (TPM or RPKM) matrix is strongly recommended !
Furthermore two additional files need to be provided, one that links the run identifiers to specific conditions. This tab delimited file should be structured as indicated below, a one-line header (which is ignored) and two columns, the first with the sample ID and the second with a short description of the condition sampled. Samples with the same description will be treated as replicates ! Omitting the condition description will exclude the sample from the profiles.
SampleID ConditionDescription
SRR068987 Endosperm
SRR314813 Seedlings, 11 DAG
SRR314814
SRR314815 Flowers (floral buds)
SRR314816
...
For profile plots on the website most likely a custom order of conditions is preferred. (We usually order tissues from bottom to top) A file to specify this needs to be provided, conditions need to be stated in the orther they should appear in the plot. Furthermore a color for that condition in the plot needs to be added in rgba() format. See the example below.
Roots (apex), 7 DAG rgba(153, 51, 0, 0.5)
Roots (differentation zone), 4 DAP rgba(153, 51, 0, 0.5)
Roots (elongation zone), 4 DAP rgba(153, 51, 0, 0.5)
Roots (meristematic zone), 4 DAP rgba(153, 51, 0, 0.5)
Roots (QC cells), 6 DAS rgba(153, 51, 0, 0.5)
Roots (stele cells), 7 DAS rgba(153, 51, 0, 0.5)
Roots (tip) rgba(153, 51, 0, 0.5)
Leaves (rosette), 21 DAG rgba(0, 153, 51, 0.5)
Leaves (rosette), 29 DAG rgba(0, 153, 51, 0.5)
...
If all files are selected click 'Add Expression Profiles' to upload the data and add everything to the database.
Adding summarized profiles
In case the complete profile is to detailed and more general profiles need to be included (useful for specificity searches), there is the option to combine multiple condition in one.
Calculating expression specificity
UNDER CONSTRUCTION