Plant
Exp
-- Zea mays --
Plant Expression Portal
Portal
Search
Blast
Comparison
Specificity
Coexpression
Cross-species
Summary
Coexpression Network Analysis
(0 Running Jobs, 12 Waiting Jobs)
Retrieve Experiments
RNA-seq
Layout
PAIRED
SINGLE
ANY
Read length(>=)
45bp
70bp
100bp
150bp
300bp
Bases(>=)
0GB
500MB
1GB
2GB
4GB
6GB
8GB
10GB
12GB
Data Source
Source
PubMed
BioProject
GEO
ANY
Reloading RNA-seq experiments
Set groups
Private experiments
Name & source
Identifier
Source
Library & sequencing
Layout
Choose layout
PAIRED
SINGLE
Read length
Volume(GB)
Sample information
Ecotype/cultivar
Genotype
Tissue
Development
Treatment
Expression level files
Gene
Transcript
Splicing profile files
JCEC
JC
Uploaded private experiments
Set trait/group labels
?
Each experiment corresponds a trait when all selected experiments are included in single group.
Trait1
Trait2
Trait3
Trait4
Trait5
Trait6
Trait7
Trait8
Trait9
Trait10
Trait11
Trait12
Trait13
Trait14
Trait15
Trait16
Trait17
Trait18
Trait19
Trait20
Co-expression (WGCNA) analysis
Gene expression
Batch effect
?
Batch effect from studies will be fit when the selected studies cover different groups simultaneously. Otherwise, batch effect from studies will be ignored.
none
study
Percentage
?
The percentage of the total genes are included for WGCNA analysis
70%
75%
80%
85%
90%
95%
100%
Alternative splicing
?
The choice doesn't affect coexpression analysis. It only affect exhibition of alternative splicing events associated with related genes.
PSI Metric
JCEC
JC
Read coverage
1
10
20
50
100
200
WGCNA setting
Expression
TPM
FPKM
Correlation
pearson
kendall
spearman
Type
unsigned
signed
Min module mize
20
25
30
35
Power
?
The power value will be set when no appropriate soft-thresholding power is picked for network construction.
6
7
8
9
10
RsquaredCut
?
The desired minimum scale free topology fitting index R^2 when picking an appropriate soft-thresholding power for network construction.
0.75
0.8
0.85
0.9
0.95
Module exhibition
Node num
?
Only the specified number of top genes will displayed in network to represent a module.
20
30
40
50
100
Node size metric
?
xxx
Connectivity
Module member-ship
Enrichment analysis
GO term
Method
EnrichGO (Hypergeometry test on AnnotationHub Annotation)
Enricher (Hypergeometry test on Genome Annotation)
P-Value
0.01
0.03
0.05
0.1
0.2
0.5
Q-value
0.01
0.03
0.05
0.1
0.2
0.5
Pathway
Method
EnrichKEGG (Hypergeometry test on KEGG Annotation)
Enricher (Hypergeometry test on KAAS Annotation)
P-Value
0.01
0.03
0.05
0.1
0.2
0.5
Q-value
0.01
0.03
0.05
0.1
0.2
0.5
Job name & E-mail
Job name
Email
