CORNET: Correlation networks: Co-expression analysis using predefined groups of microarray experiments

Step 1:

OPTION 1: one or more query genes

Paste a list of AGI codes in the text area on the left
The AGI codes may be seperated by tabs, spaces, semicolon, commas and newlines
The AGI codes are case insensitive
e.g.
at1G01010;AT1G01030;at1g01040
AT3G48750
at5g61850;at1g77950

OPTION 2: upload a file containing a list of gene pairs

Step 3: Click for guidelines

Set other options: ?

Method:
Correlation coefficient ≥ and ≤ and P-Value ≤
Top genes: (Bottom genes when comparing negative correlations)
Show:
Pairwise correlations
Correlations of query gene(s) with neighbours
Correlations between neighbours
Output:
Cytoscape (starts automatically ?)
Edge label: mean maximum minimum correlation coefficient
Text
View gene expression profiles only

STEP 3 Help (Double click to close)
Multiple expression datasets:
Expression correlation can be measured based on multiple expression datasets (selected in Step 2) simultaneously. Only the Pearson correlation coefficient is available in this option.
Pairwise comparisons:
All possible combinations between query genes are made. A correlation coefficient is calculated for each pair of genes
Neighbours:
Add extra genes. Every query gene is compared to the complete Arabidopsis genome. A gene pair with a correlation coefficient above the chosen thresholds is reported.
Thresholds:
Two thresholds can be chosen.

Correlation coefficients higher and lower than a certain value (if given) are reported.
The top X genes with highest correlation coefficients are reported, or bottom genes when comparing negative correlation coefficients. Genes with same correlation coefficients are grouped

The most limiting threshold always has priority.
(e.g. If you ask for top 10 neighbours but only 6 meet the first threshold's requirement, only 6 are shown. If you ask for top 10 neighbours but many more meet the first threshold's requirement, only 10 are shown.)

Relations between neighbours:
If you want to test if the neighbours of your query gene are co-expressed, you need to choose this option.

Cytoscape webstart Help (Double click to close)
Cytoscape will launch through JAVA™ Web Start Launcher
You may need to update JAVA™ for the Cytoscape Web Start.
Get the latest JAVA™ Runtime Environment

You can also download and install the latest version of Cytoscape locally on your computer.

Visualization legend:

*Correlation networks*
Edge color
Query gene
*Protein-protein interactions*
Edge color	black
Edge width	the more references, the wider the edge
Edge style	= experimental = predicted
Query gene
*Transcription factor interactions*
Edge color	black
Edge width	the more references, the wider the edge
Edge style	= Confirmed = Unconfirmed = Dimer
Edge arrow	= direct + Activation = direct + Repression = direct + unknown = indirect
Arrow color	green = activation red = repression black = unknown
Query gene
*COR and PPI*
Query gene
*COR and TF*
Query gene
*TF and PPI*
Query gene
*Localization pie colors* (the size of a pie slice represents how much a value is referenced compared to the others)
	CYTOSKELETON
	PEROXISOME
	OTHER
	CELLPLATE
	NUCLEOLUS
	CYTOSOL
	CHLOROPLAST
	NUCLEUS
	MITOCHONDRIA
	ENDOSOME
	PLASTID
	VACUOLE
	ENDOPLASMICRETICULUM
	EXTRACELLULAR
	PLASMAMEMBRANE
	GOLGI

Guidelines (Double click to close)

Start with stringent parameters depending on the number of query genes:
- High correlation coefficient (e.g. 0.8)
- Low number of neighbours (e.g. 10)
- Gradually loosen the stringency of the parameters
- When the co-expression network is too large, a warning will be given. A text output instead of a visual Cytoscape output can be chosen
When selecting multiple expression datasets, the number of co-expression links can rapidly increase as different expression dataset can yield complementary results (particularly for atleast=1).

Step 2:

STEP 2 Help (Double click to close)
Absolute expression values resulting from the microarray experiment
Preprocessing: RMA procedure (background correction, normalization, log2 transformation)

The CDF (Chip Description File) described in Casneuf et al. 2007 was used.

AtGenExpress All
All experiments performed by AtGenExpress

Microarray compendium 1 (454 experiments)
Collection of microarray experiments oriented towards growth, development and cell cycle studies

Microarray compendium 2 (192 experiments)
Collection of microarray experiments. Very similar experiments were removed. Similar numbers of experiments of each design type

Abiotic stress (256 exp)
Abiotic stress series (cold, drought, genotoxic, heat, osmotic, oxidative, salt, UV-B, wounding)
Biotic stress (69 exp)
Biotic stress series (Botrytis, Pseudomonas, Phytophtora, etc.)
Development (135 exp)
Developmental series (different tissues, developmental stages, developmental mutants)
Flower (72 exp)
Microarray experiments in which floral tissues are sampled
Genetic modification (313 exp)
Microarray experiments in which transgenic lines are profiled (gene overexpression (knock-in), gene knock-out, transient transgene expression)
Hormone treatment (140 exp)
Hormone treatment series (ABA, brassinosteroids, GA, cytokinin, etc. and inhibitors)
Leaf (212 exp)
Microarray experiments in which leaf tissues are sampled
Root (258 exp)
Microarray experiments in which root tissues are sampled
Seed (83 exp)
Microarray experiments in which seed tissues are sampled
Stress (abiotic+biotic) (336 exp)
Combination of the abiotic and biotic stress dataset
Whole plant (85 exp)
Microarray experiments in which whole plants are sampled

Select MicroArray data: ?

Return genes where the selection criteria are valid
in at least selected datasets:
for all selected datasets:

Abiotic stress TAIR10 (256 exp)
AtGenExpress All TAIR10 (425 exp)
Biotic stress TAIR10 (69 exp)
Development TAIR10 (135 exp)
Flower TAIR10 (72 exp)
Genetic modification TAIR10 (313 exp)
Hormone treatment TAIR10 (140 exp)
Leaf TAIR10 (212 exp)
Microarray compendium 1 TAIR10 (454 exp - bias towards cell cycle, growth, development)
Microarray compendium 2 TAIR10 (111 exp - no bias)
Root TAIR10 (258 exp)
Seed TAIR10 (83 exp)
Stress (abiotic+biotic) TAIR10 (336 exp)
Whole plant TAIR10 (85 exp)

Upload own rma data

Rma file:	(max. 200MB)
Description file:	(optional)

Please allow pop-ups. Also add: protein-protein interactions or regulatory interactions to the network localization of genes

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