Definitions of functional categories and subcategories used in the database.
Definitions and gene ontology (GO) numbers from AmiGO.

ATPase

Catalysis of the reaction: ATP + H₂O = ADP + phosphate to directly drive the transport of a substance across a membrane. GO:0043492

Cell division

The process by which a cell is partitioned and separated into daughter cells GO:0051301

Cell cycle control

A cell cycle process that modulates the rate, extent or mode of cell cycle GO:0051726

DNA replication

The process whereby new strands of DNA are synthesized. The template for replication can either be an existing DNA molecule or RNA. GO:0006260

Chromatin

The ordered and organized complex of DNA and protein that forms the chromosome GO:0000785

Chromatin remodeling

Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation GO:0006338

Chromatin structure

The specification, formation and maintenance of the physical structure of eukaryotic chromatin GO:0006325

Cytoskeletal

Any of the various filamentous elements that form the internal framework of eukaryotic cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. GO:0005856

Defense

Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. GO:0006952

Development

A biological process whose specific outcome is the progression of an integrated living unit: a cell, tissue, organ, or organism over time from an initial condition to a later condition GO:0032502

DNA repair

The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc. and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. GO:0006281

Extracellular matrix/cell wall

Any constituent part of the extracellular matrix, the structure lying external to one or more cells, which provides structural support for cells or tissues; may be completely external to the cell (as in animals or be part of the cell (as often seen in plants). GO:0031012 The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin. GO:0005618

Gene Silencing

Any mechanism, at the level of transcription or post-transcription, causing long-term gene inactivation. GO:0016458

Metabolism

Processes that cause many of the chemical changes in living organisms, including anabolism and catabolism. Metabolic processes typically transform small molecules. GO:0008152

Amino acid

The chemical reactions and pathways involving amino acids, organic acids containing one or more amino substituents, and compounds derived from amino acids. GO:0006520

Nucleotide

The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates). GO:0009117

Sugar

The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula C_x(H₂O)_y. GO:0005975

Energy

The enzymatic release of energy from organic compounds (especially carbohydrates and fats which requires oxygen as the terminal electron acceptor. GO:0009060

Lipid

The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. GO:0006629

MySEG

Mysterious SAM-expressed genes: These accessions have no significant hits with BLASTx or InterProScan and are up-regulated in SAM tissue.

No hits

These accessions have no significant hits with BLASTx or InterProScan hits and are up-regulated in the whole seedling

Other

Function is known but does not fit into any of the other categories.

Photosynthesis-related

The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO₂) using energy obtained from light rather than from the oxidation of chemical compounds. GO:0015979

Protein fate

Processes that are directly involved in protein folding, modification, degradation and/or determining cellular destination.

Protein processing and folding

The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure. GO:0006457

Protein degradation

The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. GO:0030163

Respiration

The enzymatic release of energy from organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor. GO:0009060

RNA binding protein

Interacting selectively with an RNA molecule or a portion thereof. GO:0003723

RNA processing

Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. GO:0006396

Signal transduction

Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. GO:0007165

Receptors

Combining with an extracellular or intracellular messenger to initiate a change in cell activity.

Kinases

Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate. GO:0004672

G-proteins and associated proteins

Proteins that interacting selectively with GTP, guanosine triphosphate (GO:0003924), as well as the proteins that modulate GTPase activity (GO:0030695).

Signal molecules

Phosphatases

Catalysis of the reaction: a phosphoprotein + H₂O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity. GO:0004721

Stress-related

A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GO:0006950

Transcription

The synthesis of either RNA on a template of DNA or DNA on a template of RNA. GO:0006350

Transcription factors

The function of binding to a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. GO:0003700

Transcription associated proteins

Any process that modulates the frequency, rate or extent of the synthesis of either RNA on a template of DNA or DNA on a template of RNA. GO:0045449

Translation

The chemical reactions and pathways resulting in the formation of a protein. This is a ribosome-mediated process in which the information in messenger RNA (mRNA is used to specify the sequence of amino acids in the protein.) GO:0006412

Ribosomal subunits

An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. GO:0005840

Translation-associated proteins

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. GO:0006417

Transport

The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells. GO:0006810

Transposable elements

Any process involved in mediating the movement of discrete segments of DNA between nonhomolgous sites. GO:0032196

DNA transposons

Any process involved in a type of transpositional recombination which occurs via a DNA intermediate GO:0006313

Retrotransposons

Any process involved in a type of transpositional recombination which occurs via an RNA intermediate. GO:0032197

Unknown

Gene products previously shown to be expressed, but whose function is still unknown.

Vesicle trafficking

The directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell. GO:0016192