Data & Visualizations
Visualizations for the output job data.
Volcano plot of Transcripts and Heatmap of Differentially Expressing Genes
The Volcano Plot is -Log10(Padj) vs. Log2(Fold Change). A positive Log2(Fold Change) indicates an up-regulation of a gene in condition A vs. condition B. A Log2(Fold Change) of 1 means that the gene expressed two-fold higher in condition A vs. condition B. -Log10(Padj) is a scaling metric that allows higher interpretability for the significance of results. A smaller adjusted P-value indicates higher significance. The heatmap contains centered and normalized raw read count data of Differentially Expressing Genes (DEGs) and allows for a quick overview of expression patterns by condition and gene.
NOTE: For -Log10(Padj), NaN and infinite values are automatically set to -1.
Gene Ontology Enrichment
NOTE: Initial gene ontology scan of DEGs. Not every gene has a result from our standard gene ontology process, so we provide a secondary scan in addition to this one below of all genes that did not get annotations in the first pass.
Acronym's in Category: MF - Molecular Function
Acronym's in Evidence: EXP - Experimental Evidence, IDA - Inferred from Direct Assay, IPI - Inferred from Physical Interaction, IMP - Inferred from Mutant Phenotype, IGI - Inferred from Genetic Interaction, IEP - Inferred from Expression Pattern, ISS - Inferred from Sequence or Structural Similarity, ISO - Inferred from Sequence Orthology, ISA - Inferred from Sequence Alignment, ISM - Inferred from Sequence Model, IGC - Inferred from Genomic Context, RCA - Inferred from Reviewed Computational Analysis, TAS - Traceable Author Statement, NAS - Non-traceable Author Statement, IC - Inferred by Curator, ND - No Biological Data Available
Secondary Gene Ontology Enrichment
NOTE: Secondary Gene Ontology Scan, some genes still may not have results and will require further investigation.
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Config
The configuration that was used for this job.
Configuration Setting | Set Value |
---|---|
Absolute Log2(Fold Change) Threshold | 1 |
Adjusted P-Value Threshold | 0.05000000074505806 |
Annotation Conditions Column Name | Condition |
Experimental Design Annotations | 651225330359e9e3fc2db760.xlsx |
Raw Read Counts | 651225330359e9e3fc2db75f.xlsx |
Files
The following files were either used as input(s) or produced by this job.
Output Files
Download all as a zip file:
Citations
Please cite the following if you wish to publish data produced from this job.
Muzellec, B., Telenczuk, M., Cabeli, V., & Andreux, M. (2022). PyDESeq2: a python package for bulk RNA-seq differential expression analysis. bioRxiv.
Neurosnap Inc. - Computational Biology Platform for Research. Wilmington, DE, 2022. https://neurosnap.ai/.