Building CoNekt
Using the admin panel to build CoNekt
Make sure LOGIN_ENABLED=True in config.py and the database was build with and admin account. Next, go to the website, log in and (once logged in) click on the username (admin) in the top right corner. Select 'Admin Panel' from the drop-down menu.
The Admin Panel will welcome you with a large warning. Deleting data, overwriting or changing entries here can ruin a carefully set up database. Make sure to read instructions on pages and this documentation to avoid losing work. When working with an existing database, make sure to back up the database before proceeding.
Adding GO terms and InterPro domains
Descriptions for GO terms and InterPro domains should be added before adding functional annotation. This step should be completed first. In the top menu click on 'Add' and select 'Functional Data'.
The GO descriptions can be obtained from the Gene Ontology Consortium's official website in OBO format here. InterPro domains and descriptions (called the Entry list) are found on EBI InterPro's download pages here, decompress the .gz file prior to uploading.
Click the buttons on the page and select the corresponding files, next click 'Add functional data' to upload the files to your server and import them in the database. This process can take some time, do not close the browser window.
Note: The existing tables will be cleared before adding the new definitions. Do not update this information if GO/InterPro data is already added to species !
Adding a new species and functional data
Adding a species requires multiple steps, follow the steps below for each species.
Adding the species and sequences
On the 'Admin panel', under 'Add' select 'Species'. Fill in the full scientific name (or the name you wish to appear on the website) for the species and select a 'three letter code', that is unque for the species (we recommend a combination of genus and species cfr. Homo sapiens = hsa, note that while three characters is recommended it is not required, longer codes are possible).
Some visualizations require a color specific for each species, these can be entered using the controls below (clicking the box opens a color picker, there is no need to manually add in hex values).
Finally, select a fasta file with coding sequences, in the fasta headers the gene name (and only the name) needs to be present. These are the names genes will receive on the website.
>Gene1
ATG...
>Gene2
ATG...
To upload the data and add the species to the database click 'Add species'
Adding functional Annotation to sequences
GO terms can be imported from tab delimited files, containing 3 columns: gene name, GO label and the evidence tag.
Gene1 GO:0004621 IEA
Gene1 GO:0004622 IEA
Gene2 GO:0000227 ISS
...
On the 'Admin panel', under 'Add' -> 'GO Genes' such a file can be uploaded, for a species. Additionally a description needs to be provided from where the GO terms in the file originate from (the source).
InterPro domains can be imported directly from InterProScan output. To do so, in the 'Admin panel', under 'Add' -> 'InterPro genes' select a species, select the file and click 'Add InterPro'
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 custum 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 coexpression network
UNDER CONSTRUCTION
Adding coexpression clusters
UNDER CONSTRUCTION
Adding external references
UNDER CONSTRUCTION
Computing enrichments, similarities, and counts ...
UNDER CONSTRUCTION