Genotype to phenotype, layer by layer, for the flying fish
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Coverage at each of the five layers
Each bar is one layer of the blueprint (organism-design/examples/a-flying-fish.json). A node has a direct record when a zebrafish or medaka record sits on exactly that term; derived only when records exist only on its parts and were carried upward; none when no source holds anything for it. No record means unstudied in these sources, not gene-free.
Every node
Filter by name. Numbers are distinct genes with a direct record of each type on that node: E expressed in, R required for, S sufficient for.
The pectoral fin, the organ that matters for gliding
A flying fish's "wing" is an enlarged pectoral fin. Here is everything the proxy fish say about the pectoral fin (UBERON:0000151), by link type. "Expressed in" is detection, not causation. "Required for" is a loss-of-function phenotype in a single-gene zebrafish under standard conditions. "Sufficient for" is a verified gain-of-function allele that changes the fin.
Fin size and proportion: where the flying fish is specific
Measured flying-fish fin proportions (the one flying-fish measurement set here)
Zebrafish genes with any fin size or length phenotype in ZFIN
Focus gene families from the OrthoDB figure (Tbx5, Fgf10, Shh, Hoxd13): paralogs kept apart, breadth shown
Pathway membership for every gene
Which processes and pathways each gene belongs to, from three bulk sources. Membership is not causation, and it is not even a claim about the fin.
Causal chains: gene to molecular function to process to tissue to phenotype
Each link carries its own source, organism, experiment type and an evidence grade. Grades, weakest to strongest: hypothesis, association (expression only), necessity (loss of function), sufficiency (gain of function), mechanism (a pathway step shown experimentally). A link with no fetched source is marked missing and named as a gap.
Tissue-to-tissue and cell-to-cell interactions
Directed arrows between fin tissues and cell types, for zooming into one piece of the fin. An arrow whose ligand-receptor pair comes from a human or mouse database is marked inferred by orthology.
Interventions: what genetic change moves which parameter
Manipulations that were shown in an experiment to change a fin or body measurement. A knob is calibrated only where a paper gives both a magnitude and the stage it was measured at. Most of this literature reports morphology in figure panels, so most entries carry the paper's words and no number.
Could a flying fish be made a powered flier? Hypothesis only
The physics thread specifies four changes a powered flier would need. This asks which of them has a genetic route in the literature this project fetched. It is not a predicted genome and not a design.