🧭 Plans and Withdrawn Analyses

AstroGrass Resource

Figure 2. AstroGrass catalogues five studies, OSD-375 (Brachypodium, ISS), OSD-622 (dwarf wheat, ISS), GSE97940 and GSE48040 (Brachypodium ground RNA-seq) and PXD000868 (Brachypodium leaf phosphoproteome), alongside the gravitropism candidate-gene table. The catalogue and table are served as CSV and JSON and searched in the AstroGrass database.

Added in October 2026

• Arabidopsis anchors corrected. 12 of the 29 anchor identifiers named a different gene; each was replaced, and all 29 now match their UniProt gene names.
• Orthologs. Brachypodium, rice and wheat orthologs of each anchor from Ensembl Compara (plants), with one-to-many and many-to-many cases labelled. Eight anchors have none there.
• Spaceflight values for the candidates. Taken from the per-accession DEG tables Su et al. (2023) published (CC BY 4.0) and credited to them: 13 of the 29 candidates have a DEG call.

Planned Analyses (Not Yet Run)

1. Remaining orthologs. Find Brachypodium orthologs for the eight anchors without one in Compara (LAX2, LAX3, LAZY1, DRO1, CRK28, CML24, EXPA1, CSLD1), and decide which ortholog each candidate name refers to where Compara gives several.
2. Values for genes Su et al. did not list. Needs a new differential-expression analysis from the OSD-375 FASTQ files, accounting for the confounding of accession with sequencing batch.
3. Gravitropism measurements. Add numeric measurements for the accession panel, with their source documented.
4. Association with genotype. Needs genotype data for the phenotyped accessions; with tens of accessions it would be a candidate-gene comparison rather than a GWAS.
5. Comparison with Arabidopsis. Compare with the author's Arabidopsis spaceflight analysis, which is in preparation, once its consensus gene set can be regenerated from code.

Withdrawn on 14 October 2026

These results appeared on this site and in the draft manuscript. None came from an analysis, so they were removed:

• The 15-accession gravitropic curvature survey and its ANOVA, and the 46-accession correlation figure: the values were generated from seeded random numbers.
• The GWAS Manhattan and QQ plots: random p-values with named genes typed in as peaks; no genotype data existed.
• Gene-level spaceflight fold changes, adjusted p-values, DEG counts and the volcano and enrichment panels for OSD-375: typed-in values; no differential-expression analysis was run.
• The cross-species meta-analysis with Arabidopsis (odds ratio 13.70, p = 0.0446; and odds ratio 14.16, p = 3.54 × 10⁻¹²): computed from hand-entered flags.
• The cereal synteny map and table, the promoter-motif enrichment and the alternative-splicing tables: typed-in values.
• The mechanistic model's spaceflight panel, which listed up- and down-regulated genes taken from the typed-in values.
• The Brachypodium gene IDs, chromosome positions and rice/wheat orthologs of the candidate genes: none of the IDs is an ortholog of its Arabidopsis anchor in Ensembl Compara. They were replaced by Compara orthologs.