Switchgrass RNA-seq Browser

Enter a gene identifier or annotation term to begin.

Selected gene

Expression across cold acclimation

Biological replicates and group means from the common-reference featureCounts matrix.

Display

AP13 · lowland VS16 · upland biological replicate

Chart scale: log2(CPM + 1) is normalized expression abundance for visualization. It is not a DESeq2 log2 fold change and does not by itself indicate statistical significance.

Exact expression values

Differential expression

Only rows passing adjusted P < 0.05 in the supplied DE results are shown. A missing comparison is not evidence of equal expression.

Contrasts

How to read every row: “A vs B” means log2(A/B). A positive value means higher expression in A; a negative value means higher expression in B. The table states the higher condition beneath each value.

Formal result: this is the DESeq2 log2 fold change from the supplied analysis, not the log2(CPM + 1) value used in the expression chart.

Haplotype-biased expression

Informative-SNP read support is shown separately from total gene expression. Calls require adequate read support and replicate agreement.

HAP1 read share HAP2 read share

Annotation

Data scope

What this browser uses—and what each measurement means

This public browser is source-backed and reads a deployment copy of the analysis database. It does not alter the underlying analysis files.

Experimental design

Thirty biological samples cover five ordered conditions (NonA, 4h, 1d, 4d, 7d), two ecotypes (AP13 lowland and VS16 upland), and three biological replicates per ecotype-time group.

Total gene expression

The chart uses raw paired-end fragment counts from the AP13 HAP1 v6.1 featureCounts matrix. Each sample is divided by its assigned-fragment library size and multiplied by one million to produce CPM. This supports within-gene comparisons across samples and time.

CPM means counts per million assigned fragments. The default display applies log2(CPM + 1) so zero-expression observations can be shown and large expression ranges fit on one chart. These values are expression abundances, not fold changes.

Caution: AP13 HAP1 is a common reference for both ecotypes. Sequence divergence can create reference-alignment bias. Use the supplied differential-expression results for formal AP13-vs-VS16 inference and treat the CPM chart as an exploratory expression profile.

Differential expression

The browser imports the supplied rnaseq_all_comparisons_DE.csv. Every imported row has adjusted P ≤ 0.05; this is a significant-results table rather than a complete all-tested-gene table.

The readable comparison is shown as numerator vs denominator: positive DESeq2 log2FC means the numerator is higher, and negative means the denominator is higher. The original comparison code remains beneath the readable label for traceability. The supplied legacy codes for 4hvs1d and 4hvs4d use the opposite sign order from most within-ecotype codes, so the browser explicitly displays their verified biological direction.

Haplotype bias

The bias view uses strict one-to-one HAP1/HAP2 gene pairs across both AP13 and VS16 and all five time points. HAP1/HAP2 counts represent reads overlapping informative SNPs, not total transcript abundance. Low-total rows are shown explicitly so absence of evidence is not mistaken for balance.

Data readiness

Website feature	Source	Readiness
Gene and annotation search	v5.1↔haplotype mapping plus UniProt/GO fields	Ready
Five-timepoint expression	AP13 HAP1 v6.1 featureCounts, 30 samples	Ready for exploratory CPM profiles
Differential expression	343,326 significant gene-comparison rows	Ready
Haplotype bias	486,310 gene-context-time rows	Ready
Transcript-level expression	No transcript abundance matrix in the current browser inputs	Future extension