# Coral Transcriptome Explorer — Help

An interactive browser for the **PDLTTE** (*Pocillopora acuta* long-term thermal
experiment; Mayfield et al. 2014, *Mol. Ecol.*, doi:10.5061/dryad.rh04m) and
**SHVTS** (*Seriatopora hystrix* variable-temperature study; Mayfield et al. 2016,
*Mol. Ecol.*) holobiont transcriptomes.

## Datasets (tabs)
Each species splits into three compartments, resolved from per-contig BLAST taxonomy:
- **host** — the coral host transcriptome
- **Symbiodiniaceae** — the dinoflagellate endosymbiont within the same RNA pool
- **holobiont (all)** — host + Symbiodiniaceae + other microbes together

## Comparisons
Use the **Active comparison** selector to switch the differential-expression contrast.
- **PDLTTE:** Temperature (30 °C vs 27 °C) · Time (36 wk vs 2 wk) · Temperature × Time interaction
- **SHVTS:** Treatment (variable vs stable) · Site of origin (Houwan vs Houbihu) · Site × Treatment interaction

Main effects use Welch's *t*-test on log₂ FPKM; interactions use the 2-way ANOVA
interaction term (effect size = difference of the two simple fold-changes). The
volcano plot, heatmap, and table all update to the selected contrast.

## Normalize to host : Symbiodiniaceae ratio
Because the host : Symbiodiniaceae cell ratio differs between samples, a Symbiodiniaceae gene's raw
FPKM partly reflects *how much Symbiodiniaceae was present*, not its per-cell expression.
Ticking **Normalize to host : Symbiodiniaceae ratio** rescales each sample so its host- and
Symbiodiniaceae-transcriptome totals match the cross-sample mean, removing that confound
(after Mayfield et al. 2014). The effect is largest for Symbiodiniaceae genes — some
fold-changes change sign once Symbiodiniaceae load is controlled for.

## Tools
- **Annotation Search** / **KEGG Pathways** — find genes by name, KO, or GO.
- **BLAST** — search your sequence against the host / Symbiodiniaceae protein (and, where
  built, nucleotide) databases. *Requires the backend server.*
- **Proteomics (MS-GF+)** — upload an mzML to search spectra against the protein
  databases at 1 % FDR. *Requires the backend server.*
- **Download** — export the filtered table as **TSV** or an annotated **FASTA**
  (client = the loaded top-variance + DE subset; server = the complete filtered set).

## qPCR assays
Genes for which a qPCR assay was designed show a **🧫 qPCR** link in the Expression
Table; click it to download the primer/sequence file.

## Host genotype
The PDLTTE host coral genotype (mitochondrial ORF alignment vs *P. damicornis*
mitogenomes) is available under **Reference data**.

## Hosting note
The explorer + data files are static and can be hosted anywhere (e.g. Lightsail or
S3) and iframe-embedded into the website. Only **BLAST** and **MS-GF+** need the live
Flask backend (`transcriptome_server.py`, `proteomics_server.py`) — run it on
Lightsail (always-on) rather than the laptop+ngrok so those tools stay up.