Table 1 Glossary of common terms that were used in this study

Degree of connectivity

Identification of how well a node is connected in a network. For example, if a network has 10 nodes and a node is connected to 5 nodes, it’s degree of connectivty is 0.5.

Desiccation tolerance (DT) phase

The last phase in developing embryos characterized by loss of water, a sharp increase of desiccation-related metabolites and transcripts, and acquisition of DT in yellow embryos at day 55.

Differentially expressed transcript

A transcript that was significantly differentially expressed at at least one time point compared with previous time point (FDR < 0.05).

Domain categorization

The domain composition of SV-pairs were compared and categorized into similar domains, no known domain, and disparate domains.

Early maturation phase

This first phase in seed filling is characterized by an initial decrease in metabolites and cell-division-related transcript levels and the onset of accumulation of seed storage compounds.

Expressed transcripts

A transcript was defined as expressed if the sum of its FPKM values across the time course was greater than one.

Hub

Highly connected nodes in a network (nodes with the highest degree of connectivity).

Mid-to-late maturation phase

This phase in embryo development is characterized by a stable accumulation of seed storage compounds.

Nearest neighbors

Nodes directly connected through individual edges to a single node of interest.

Regulon

A group of transcripts known to be targets of a common TF. For example, a group of transcripts known to be targets of ABI3, is called the ABI3 regulon.

Soybean developmental stages

Three major developmental stages (early maturation, mid-to-late maturation, and DT) defined in this report on the basis of changes in the levels of relevant metabolites, seed storage compounds, and transcripts in developing soybean embryos.

Splice variant (SV)

Transcripts that are products of the same precursor mRNA.

Sub-network

A group of nodes and edges that are part of a larger network. For example, a node with all its nearest neighbors comprising the members of the FUS3 regulon is a sub-network.

Super-cluster

Clusters of transcripts with similar expression profiles grouped according to predefined soybean developmental stages.

SV group

A group containing at least two SVs of a gene both of which were significantly differentially expressed during embryo development. For example, gene X has three SVs (X.1, X.2, X.3), and X.1 and X.3 showed changes in transcript levels and X.2 was stably expressed in developing embryos. X.1 and X.3 belong to the same SV group representing gene X.