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Karyoptyping

L

M

  • MAGEMicroArray and Gene Expression, a group that "aims to provide a standard for the representation of DNA microarray gene expression data that would facilitate the exchange of microarray information between different data systems".[3]
  • MIAME – a commercial standard developed by FGED based on MAGE to facilitate storage and sharing of gene expression data It stands for Minimum information about a microarray experiment.[4][5]
  • MINSEQE – commercial standard developed by FGED for storage and sharing of high-throughput sequencing data. It stands for Minimal Information about a high-throughput SEQuencing Experiment.[6]
  • MGED – former name of the FGED Society.

N

  • NBF or Neutral Buffer Formalin – a common solution used in the fixation of cells or cellular tissue for marking and study.

O

P

  • Probe – a term to describe a reagent used to make a single measurement in a gene expression experiment. See reporter, probe-set.
  • Probe-set – a collection of two or more probes that are designed to measure a single molecular species. For example, several oligonucleotides designed to hybrize to various parts of the mRNA generated from a single gene.
  • Promoter – a region of DNA that initiates the transcription of a particular gene.
  • Promotion – increasing the rate of gene expression.
  • Putative genes – a nucleotide sequence thought to be a gene based on the identification of its open reading frame (ORF). The gene is "putative" in the sense that no function has been assigned to its products.

Q

R

  • Regulation of gene expression – the cell's system for controlling the expression of genes.
  • Replication – a technique to estimate technical and biological variation in experiments for statistical analysis of the microarray data. Replicates may be:
    • technical replicates, such as dye swaps or repeated array hybridizations, or
    • biological replicates, using biological samples from separate experiments that test the effects of the same treatments.
  • Reporter – a MIAMI-compliant term to describe a reagent used to make a single measurement in a gene expression experiment. MIAMI defines it as "the nucleotide sequence present in a particular location on the array".[4] A Reporter may be single-stranded DNA that is covalently attached to the array surface. See probe or probe-set.
  • Repression – decreasing the rate of gene expression.
  • Repressor – a DNA-binding protein that regulates the expression of one or more genes by binding to the operator and blocking the attachment of RNA polymerase to the promoter, thus preventing transcription of the genes.
  • RNA splicing – modification of an RNA strand where exons (the coding regions of a transcribed gene) are retained and the introns are removed. Sometimes the exons are recombined either in vivo or experimentally to form alternative splicings, which have various functional effects.

S

  • Signal transduction pathway – a set of biochemical reactions and biomolecular interactions that convert a stimulus into a metabolic response. A signaling molecule initially binds to a receptor on the surface of the cell, which stimulates the activation of immediate early genes and second messenger molecules. This further activates enzymes that carry out larger-scale processes such as phosphorylation and gene expression. The process just described is known as a signaling cascade, during which the initial stimulus is amplified to have a far-reaching effect on the cellular environment.
  • Silencer – A region of DNA that can be bound by Repressors.
  • Signature – refers to the set of expression measurements which satisfy a certain arbitrary threshold criteria, such as 1.5 fold change with a significance p<0.01. Analysts may define a signature for a given experiment or compare gene signatures across many experiments.
  • Spatially-restricted gene expression – genes that are expressed only in a specific anatomical region or tissue, often in response to a paracrine signal. The boundary between two spatially-restricted genes can set up a sharp gradient, often expressed phenotypically as striping patterns.
  • Suppression – decreasing the rate of gene expression. See Down-regulation

T

  • Tissue-specific expression – Gene function and expression which is restricted to a particular tissue or cell type. For example, the glycoprotein hormone alpha subunit is produced only in certain cell types of the anterior pituitary and placenta, not in lungs or skin; thus expression of the glycoprotein hormone alpha-chain gene is said to be tissue-specific. Tissue specific expression is usually the result of an enhancer which is activated only in the proper cell type.
  • Transcriptional bursting – transcription (and also translation) occurs in "bursts" or "pulses", with periods of gene activity separated by irregular intervals.
  • Transcription factor – a protein that binds to specific DNA sequences, thereby controlling the rate of transcription of genetic information from DNA to messenger RNA

U

  • Up regulation – increasing the rate of gene expression.
  • Up-regulated – describes a gene which has been observed to have higher expression (higher mRNA levels) in one sample compared to another (usually the control).

V

W

X

Y

Z

Z form gene.

References

  1. ^ Priness, I.; Maimon, O.; Ben-Gal, I. (2007). "Evaluation of gene-expression clustering via mutual information distance measure". BMC Bioinformatics. 8: 111. doi:10.1186/1471-2105-8-111. PMC 1858704Freely accessible. PMID 17397530. 
  2. ^ "Functional Genomics Data Society – FGED Society". 
  3. ^ Rayner TF; Rocca-Serra P; Spellman PT; Causton HC; et al. (2006). "A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB". BMC Bioinformatics. 7: 489. doi:10.1186/1471-2105-7-489. PMC 1687205Freely accessible. PMID 17087822. 
  4. ^ a b Oliver S (2003). "On the MIAME Standards and Central Repositories of Microarray Data". Comp. Funct. Genomics. 4 (1): 1. doi:10.1002/cfg.238. PMC 2447402Freely accessible. PMID 18629115. 
  5. ^ Brazma A (2009). "Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges". ScientificWorldJournal. 9: 420–3. doi:10.1100/tsw.2009.57. PMID 19484163. 
  6. ^ Functional Genomics Data Society (June 2012). "Minimum Information about a high-throughput SEQuencing Experiment". 
  7. ^ "overexpression". Oxford Living Dictionary. Oxford University Press. 2017. Retrieved 18 May 2017. The production of abnormally large amounts of a substance which is coded for by a particular gene or group of genes; the appearance in the phenotype to an abnormally high degree of a character or effect attributed to a particular gene. 
  8. ^ "overexpress". NCI Dictionary of Cancer Terms. National Cancer Institute at the National Institutes of Health. Retrieved 18 May 2017. overexpress
    In biology, to make too many copies of a protein or other substance. Overexpression of certain proteins or other substances may play a role in cancer development.