PlantExp -- FAQ --
Plant Expression Portal

Frequently Asked Questions (and Answers)

Q: How to download gene expression levels and alternative splicing profiles?
A: These data can be downloaded on the summary page of each species.
Q: What's the difference between JCEC and JC PSI?
A: JCEC PSI is calculated using both reads that span junctions defined by rMATS (Junction Counts) and reads that do not cross an exon boundary (Exon Counts). While JC PSI is calculated using only reads that span junctions (Junction Counts).
Q: Does selected differential expression metric affect the results of differential/specifical expression analysis?
A: No. Differential/specifical expression analysis is based on read count rather than expression level.
Q: Why does the job of differential/specifical expression analysis need to be confirmed by email?
A: Analysis task consumes lots of computing resource, so we have to ensure that an analysis job comes from manual submission instead of machine.
Q: Why a job does not run after submission through my email?
A: Each job is in the queue before it starts.
Q: Why I can't request an analysis job by a correct email?
A: You may have unfinished jobs under this email account.
Q: Why are there only two GO/pathway enrichment methods for some species?
A: No annotation in AnnotationHub will cause EnrichGO and gseGO invalid. No pathway annotaion in KEGG database will cause EnrichKEGG and gseKEGG invalid.
Q: Must read lengths of RNA-seq experiments be identical in differential/specifical splicing analysis?
A: Yes, only reads with identical length can ensure the accuracy of splicing analysis, which is also mandatory when using rMATS. If read lengths are not identical, PlantExp will report this type of message. If you continue to submit, one of the read lengths will be used in the analysis, which is unaccurate and not recommended.
Q: What's the difference between MATS_LRT, rMATS_unpaired and rMATS_paired?
A: In MATS_LRT model, read counts of all replicates in a group are added together. rMATS_unpaired model is used on replicates without pairs between groups. rMATS_paired is used when each replicate is paired with another between the two sample groups.
Q: How to obtain the expression of homologus gene?
A: Two approaches are available. 1) The user can enter gene sequence in the blast page of concerned species to search homologus gene expression. 2) In the gene page, the user can click the Orthogroup ID to open a popup page to explore gene expression of corresponding orthologues in other species.
Q: Can I upload raw data files(fastq) to perform a co-analysis task?
A: No, given the limitations of network speed and computing resources, the platform only accepts gene expression and alternative splicing data.