SPELL - Nematode

The tags used to describe the datasets on this website have the definitions indicated in the following table.

The tags were selected based on the areas of biology investigated in the associated publications. These tags comprise a controlled vocabulary (CV) of terms synthesized and defined to cover the range of perturbations employed in the microarray experiments. These perturbations include chemical treatments, alterations in nutritional conditions, challenge with physical insult and/or changes in the genetic background due to mutation. The tags provide a means of selecting and grouping datasets based on the perturbation(s).

CV term name Definition

Method: microarray microarray

Method: RNAseq RNAseq

Method: proteomics proteomics

Method: tiling array tiling array

Species: Caenorhabditis elegans Caenorhabditis elegans

Species: Caenorhabditis brenneri Caenorhabditis brenneri

Species: Caenorhabditis. briggsae Caenorhabditis briggsae

Species: Caenorhabditis japonica Caenorhabditis japonica

Species: Caenorhabditis remanei Caenorhabditis remanei

Species: Onchocerca volvulus Onchocerca volvulus

Species: Pristionchus. pacificus Pristionchus. pacificus

Species: Strongyloides ratti Strongyloides ratti

Species: Brugia malayi Brugia malayi

Topic: aging A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).

Topic: response to hypoxia Any process that results in 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 lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.

Topic: DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

Topic: 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.

Topic: lipid metabolic process 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.

Topic: response to osmotic stress Any process that results in 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 an increase or decrease in the concentration of solutes outside the organism or cell.

Topic: response to unfolded protein Any process that results in 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 an unfolded protein stimulus.

Topic: dosage compensation Compensating for the variation in the unpaired sex chromosome:autosome chromosome ratios between sexes by activation or inactivation of genes on one or both of the sex chromosomes.

Topic: response to temperature stimulus Any process that results in 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 temperature stimulus.

Topic: response to temperature stimulus response to temperature stimulus

Topic: response to radiation Any process that results in 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 an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.

Topic: embryo development The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.

Topic: programmed cell death A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.

Topic: RNA interference The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes.

Topic: gene silencing by miRNA Downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: endolytic cleavage of mRNA cleavage or translational repression, usually accompanied by poly-A tail shortening and subsequent degradation of the mRNA.

Topic: dauer larval development The process whose specific outcome is the progression of the dauer larva over time, through the facultative diapause of the dauer (enduring) larval stage, with specialized traits adapted for dispersal and long-term survival, with elevated stress resistance and without feeding.

Topic: vulval development The process whose specific outcome is the progression of the egg-laying organ of female and hermaphrodite nematodes over time, from its formation to the mature structure. In nematodes, the vulva is formed from ventral epidermal cells during larval stages to give rise to a fully formed vulva in the adult.

Topic: response to chemical Any process that results in 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 chemical stimulus.

Topic: response to starvation Any process that results in 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 starvation stimulus, deprivation of nourishment.

Topic: innate immune response Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.

Topic: developmental time course developmental time course

Topic: disease disease

Topic: gene expression - general gene expression - general

Topic: natural variant natural variant

Topic: space flight space flight

Topic: Tissue Specific: alimentary system Tissue Specific: alimentary system

Topic: Tissue Specific: germline Tissue Specific: germline

Topic: Tissue Specific: muscle Tissue Specific: muscle

Topic: Tissue Specific: neuron Tissue Specific: neuron

Topic: Tissue Specific: other Tissue Specific: other

Topic: Tissue Specific: reproductive system Tissue Specific: reproductive system

Topic: unclassified unclassified

CV term name	Definition
Method: microarray	microarray
Method: RNAseq	RNAseq
Method: proteomics	proteomics
Method: tiling array	tiling array
Species: Caenorhabditis elegans	Caenorhabditis elegans
Species: Caenorhabditis brenneri	Caenorhabditis brenneri
Species: Caenorhabditis. briggsae	Caenorhabditis briggsae
Species: Caenorhabditis japonica	Caenorhabditis japonica
Species: Caenorhabditis remanei	Caenorhabditis remanei
Species: Onchocerca volvulus	Onchocerca volvulus
Species: Pristionchus. pacificus	Pristionchus. pacificus
Species: Strongyloides ratti	Strongyloides ratti
Species: Brugia malayi	Brugia malayi
Topic: aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
Topic: response to hypoxia	Any process that results in 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 lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
Topic: DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
Topic: 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.
Topic: lipid metabolic process	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.
Topic: response to osmotic stress	Any process that results in 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 an increase or decrease in the concentration of solutes outside the organism or cell.
Topic: response to unfolded protein	Any process that results in 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 an unfolded protein stimulus.
Topic: dosage compensation	Compensating for the variation in the unpaired sex chromosome:autosome chromosome ratios between sexes by activation or inactivation of genes on one or both of the sex chromosomes.
Topic: response to temperature stimulus	Any process that results in 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 temperature stimulus.
Topic: response to temperature stimulus	response to temperature stimulus
Topic: response to radiation	Any process that results in 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 an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
Topic: embryo development	The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
Topic: programmed cell death	A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
Topic: RNA interference	The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes.
Topic: gene silencing by miRNA	Downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: endolytic cleavage of mRNA cleavage or translational repression, usually accompanied by poly-A tail shortening and subsequent degradation of the mRNA.
Topic: dauer larval development	The process whose specific outcome is the progression of the dauer larva over time, through the facultative diapause of the dauer (enduring) larval stage, with specialized traits adapted for dispersal and long-term survival, with elevated stress resistance and without feeding.
Topic: vulval development	The process whose specific outcome is the progression of the egg-laying organ of female and hermaphrodite nematodes over time, from its formation to the mature structure. In nematodes, the vulva is formed from ventral epidermal cells during larval stages to give rise to a fully formed vulva in the adult.
Topic: response to chemical	Any process that results in 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 chemical stimulus.
Topic: response to starvation	Any process that results in 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 starvation stimulus, deprivation of nourishment.
Topic: innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
Topic: developmental time course	developmental time course
Topic: disease	disease
Topic: gene expression - general	gene expression - general
Topic: natural variant	natural variant
Topic: space flight	space flight
Topic: Tissue Specific: alimentary system	Tissue Specific: alimentary system
Topic: Tissue Specific: germline	Tissue Specific: germline
Topic: Tissue Specific: muscle	Tissue Specific: muscle
Topic: Tissue Specific: neuron	Tissue Specific: neuron
Topic: Tissue Specific: other	Tissue Specific: other
Topic: Tissue Specific: reproductive system	Tissue Specific: reproductive system
Topic: unclassified	unclassified