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Exp
-- Caenorhabditis elegans --
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Differential Expression Analysis
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Retrieve Experiments
RNA-seq
Layout
PAIRED
SINGLE
ANY
Read length(>=)
30bp
45bp
70bp
100bp
150bp
300bp
Volume(>=)
0GB
500MB
1GB
2GB
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8GB
10GB
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Data source
Source
PubMed
BioProject
GEO
ANY
Loading RNA-seq experiments
Set groups
Group setting
Control
No experiments selected
Treatment
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Differential analysis
Expression
Method
DESeq2
edgeR
Fold-Change
2
4
8
16
Q-Value
0.01
0.03
0.05
0.1
0.2
0.5
Counts per million(CPM)
?
It is used to filter un/low-expressed genes out. Only the genes with a specified number of reads in per million mapped reads are included in differential expression analysis. For example, for a 3- and 4-sample comparison, if only genes with specified CPM value in at least 3 samples, it will be included in differential expression analysis.
1
10
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200
Model
exact test
likelihood ratio test
quasi-likelihood F test
Batch effect
?
Batch effect from studies can be fit when the selected studies cover control and treatment simultaneously. Otherwise, batch effect from studies will be ignored.
none
study
Metric
TPM
?
Transcripts Per Million (TPM) is a normalization method for RNA-seq, should be read as "for every 1,000,000 RNA molecules in the RNA-seq sample, x came from this gene/transcript."
FPKM
?
Fragments Per Kilobase of transcript per Million mapped reads(FPKM) is a expression level normalization method which normalizes read count based on gene length and the total number of mapped reads.
Splicing
Method
MATS_LRT
rMATS_unpaired
rMATS_paired
PSI-Change
0.05
0.1
0.2
0.4
0.8
Q-Value
0.01
0.03
0.05
0.1
0.2
0.5
Splicing read coverage
?
Only alternative splicing events with enough read coverage are included in differential splicing analysis.
1
10
20
50
100
200
Metric
JCEC
?
The PSI value is calculated including both reads that span junctions defined by rmats (Junction Counts) and reads that do not cross an exon boundary (Exon Counts).
JC
?
The PSI value is calculated including only reads that span junctions defined by rmats (Junction Counts)
Enrichment analysis
GO term
Method
EnrichGO (Hypergeometry test on AnnotationHub Annotation)
Enricher (Hypergeometry test Genome Annotation)
gseGO (Gene Set Enrichment Analysis on AnnotationHub Annotation)
GSEA (Gene Set Enrichment Analysis 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)
gseKEGG (Gene Set Enrichment Analysison KEGG Annotation)
GSEA (Gene Set Enrichment Analysis on KAAS AnnotationHub)
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 and E-mail
Job name
Email