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  • sequences
  • Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. (rna-seqblog.com)
  • profiles
  • To compare the microRNA (miRNA) expression profiles in neurons and innervated muscles after sciatic nerve entrapment using a non-constrictive silastic tube, subsequent surgical decompression, and denervation injury. (nih.gov)
  • We tested reproducibility by comparing the expression profiles provided by U133 Plus 2.0 GeneChips® for 3 independently amplified RNA samples: a high degree of correlation between the replicates was obtained. (unimi.it)
  • robust
  • CONCLUSIONS: Hereby we present a publicly available tool for robust characterization of Arabidopsis gene expression experiments which can point to similar experimental factors in other experiments. (dtu.dk)
  • variable
  • Using as their benchmarks the known transcripts from these well-annotated genomes (sequenced a decade ago), they assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as alternative splicing and variable expression levels. (rna-seqblog.com)
  • protein
  • This is due to alternative splicing , and also because cells make important changes to proteins through posttranslational modification after they first construct them, so a given gene serves as the basis for many possible versions of a particular protein. (wikipedia.org)
  • An expression system refers to the factors that work together to yield a particular gene product such as a protein, ribozyme or RNA particle. (news-medical.net)
  • The expression system is made up of a gene, which is encoded by DNA, and the machinery needed to make mRNA from the DNA and translate that into a protein. (news-medical.net)
  • Virtually any step of gene expression can be modulated, from transcriptional initiation , to RNA processing , and to the post-translational modification of a protein. (wikipedia.org)
  • Any step of gene expression may be modulated, from the DNA-RNA transcription step to post-translational modification of a protein. (wikipedia.org)
  • These products are often proteins, but in non-protein coding genes such as transfer RNA (tRNA) or small nuclear RNA (snRNA) genes, the product is a functional RNA. (wikipedia.org)
  • Several steps in the gene expression process may be modulated, including the transcription, RNA splicing, translation, and post-translational modification of a protein. (wikipedia.org)
  • RNA polymerase II (Pol II) transcribes all protein-coding genes but also some non-coding RNAs (e.g., snRNAs, snoRNAs or long non-coding RNAs). (wikipedia.org)
  • While transcription of prokaryotic protein-coding genes creates messenger RNA (mRNA) that is ready for translation into protein, transcription of eukaryotic genes leaves a primary transcript of RNA (pre-mRNA), which first has to undergo a series of modifications to become a mature mRNA. (wikipedia.org)
  • For example, the reporter gene green fluorescent protein can be visualized by stimulating it with blue light and then using a digital camera to record green fluorescent emission. (wikipedia.org)
  • Immunohistochemistry involves preparing an antibody with specific affinity for the protein associated with the gene of interest. (wikipedia.org)
  • Furthermore, since immunohistochemistry visualizes the protein generated by the gene, if the protein product diffuses between cells, or has a particularly short or long half-life relative to the mRNA that is used to translate the protein, this can lead to distorted interpretation of which cells are expressing the mRNA. (wikipedia.org)
  • The following is a list of stages where gene expression is regulated, the most extensively utilised point is Transcription Initiation: Chromatin domains Transcription Post-transcriptional modification RNA transport Translation mRNA degradation In eukaryotes, the accessibility of large regions of DNA can depend on its chromatin structure, which can be altered as a result of histone modifications directed by DNA methylation, ncRNA, or DNA-binding protein. (wikipedia.org)
  • Both proteins bind to single-stranded DNA as well as to RNA and can stimulate the activity of RNA polymerase II, the protein responsible for most gene transcription. (wikipedia.org)
  • Protein K has been the subject of study related to colorectal cancer, in which an RNA editing event inducing the expression of an isoform containing a point mutation was found to be specific to cancerous cells. (wikipedia.org)
  • Corepressor - A protein that reduces (represses) the expression of genes by binding to and activating a repressor transcription factor. (wikipedia.org)
  • Expression of the heat shock protein IpbA in species of Pseudomonas is controlled by a ROSE-type RNA thermometer. (wikipedia.org)
  • Gene co-expression networks are of biological interest since co-expressed genes are controlled by the same transcriptional regulatory program, functionally related, or members of the same pathway or protein complex. (wikipedia.org)
  • 2007). Interestingly, the immunoglobulin lambda light chain locus contains protein-coding genes that can be lost with its rearrangement. (wikipedia.org)
  • chromosome
  • An example of a chromosome with two genes, each of size 9, is the string (position zero indicates the start of each gene): 012345678012345678 L+a-baccd**cLabacd where "L" represents the natural logarithm function and "a", "b", "c", and "d" represent the variables and constants used in a problem. (wikipedia.org)
  • mRNA expression
  • The hormone level differences between males and destrous females can be shown by the differences in Kiss 1 mRNA expression between male and female rats during their neonatal period (time period between existing in the maternal uterus and existing completely independently). (wikipedia.org)
  • The lactase persistent phenotype involves high mRNA expression, high lactase activity, and thus the ability to digest lactose, while the lactase nonpersistent phenotype involves low mRNA expression and low lactase activity. (wikipedia.org)
  • proteins
  • While knowledge of the precise proteins a cell makes ( proteomics ) is more relevant than knowing how much messenger RNA is made from each gene, gene expression profiling provides the most global picture possible in a single experiment. (wikipedia.org)
  • Kisspeptins are a group of proteins that come from precursors that are approximately 145 amino acids in length that get reduced to 54 and then finally about 10, 13, or 14 amino acid carboxyl terminals and are encoded by the Kiss 1 gene and are thought to be involved in the initiation of puberty by stimulating the release of the gonadotropin-releasing hormone (GnRH). (wikipedia.org)
  • The rearrangement and organization of these gene segments during the maturation of B cells produce functional proteins.The entire process of rearrangement and organization of these gene segments is the vital source where our body immune system gets its capabilities to recognize and respond to variety of antigens. (wikipedia.org)
  • existing cluster
  • A popular approach to class discovery involves grouping similar genes or samples together using one of the many existing clustering methods such the traditional k-means or hierarchical clustering , or the more recent MCL and clust methods. (wikipedia.org)
  • tumor
  • For example, a normal tissue sample can be compared against a corresponding tumor to determine which genes tend to be more (or less) active. (wikipedia.org)
  • Because of these selective properties, the majority of cells within a tumor will share a common profile of gene expression. (wikipedia.org)
  • Of note, similar gene expression patterns associated with metastatic behaviour of breast cancer tumor cells have also been found in breast cancer of dog, the most common tumor of the female dog. (wikipedia.org)
  • whereas
  • whereas in a gene regulatory network (GRN) a directed edge connects two genes, representing a biochemical process such as a reaction, transformation, interaction, activation or inhibition. (wikipedia.org)
  • Reporter
  • The expression distribution of the reporter gene can be determined by visualizing it. (wikipedia.org)
  • Reporter genes can be visualized in living organisms, but both immunohistochemistry and in situ hybridization must be performed in fixed tissues. (wikipedia.org)
  • typically
  • Housekeeping gene - typically a constitutive gene that is transcribed at a relatively constant level across many or all known conditions. (wikipedia.org)
  • transcript
  • With respect to a gene, the two strands may be labeled the "template strand," which serves as a blueprint for the production of an RNA transcript, and the "coding strand," which includes the DNA version of the transcript sequence. (wikipedia.org)
  • nodes
  • A gene co-expression network (GCN) is an undirected graph, where each node corresponds to a gene, and a pair of nodes is connected with an edge if there is a significant co-expression relationship between them. (wikipedia.org)
  • involves
  • A popular approach to class discovery involves grouping similar genes or samples together using k-means or hierarchical clustering. (wikipedia.org)
  • tissue
  • In situ hybridization is an alternate method in which a "probe," a synthetic nucleic acid with a sequence complementary to the mRNA of the gene, is added to the tissue. (wikipedia.org)
  • known
  • Most early expression profiling experiments, and many current ones, have this form which is known as class discovery. (wikipedia.org)
  • Current cancer research makes use primarily of DNA microarrays in which an arrayed series of microscopic spots of pre-defined DNA oligonucleotides known as probes are covalently attached to a solid surface such as glass, forming what is known as a gene chip. (wikipedia.org)
  • similar
  • The figure above represents the output of a two dimensional cluster, in which similar samples (rows, above) and similar gene probes (columns) were organized so that they would lie close together. (wikipedia.org)
  • Each element in this matrix shows how similar the expression level of two genes change together. (wikipedia.org)
  • Heavy chain contains similar gene segments such as VH, JH and CH, but also has another gene segment called D (diversity). (wikipedia.org)
  • represents
  • For example, the mathematical expression: ( a − b ) ( c + d ) {\displaystyle {\sqrt {(a-b)(c+d)}}\,} can also be represented as an expression tree: where "Q" represents the square root function. (wikipedia.org)
  • The resulting matrix, called adjacency matrix, represents the graph of the constructed gene co-expression network. (wikipedia.org)
  • messenger
  • For example, in the case of embryonic Drosophila development, the genes nanos and bicoid are asymmetrically expressed in the oocyte because maternal cells deposit messenger RNA (mRNA) for these genes in the poles of the egg before it is laid. (wikipedia.org)
  • Cap analysis gene expression (CAGE) is a technique used in molecular biology to produce a snapshot of the 5′ end of the messenger RNA population in a biological sample. (wikipedia.org)
  • biology
  • Sophisticated programs of gene expression are widely observed in biology, for example to trigger developmental pathways , respond to environmental stimuli, or adapt to new food sources. (wikipedia.org)
  • level
  • Baseline - a measure of the gene expression level of a gene or genes prior to a perturbation in an experiment, as in a negative control. (wikipedia.org)
  • Random rearrangements and recombinations of the gene segments at DNA level to form one kappa or lambda light chain occurs in an orderly fashion. (wikipedia.org)