Gene expression

RNA-Seq (RNA sequencing), also called whole transcriptome shotgun sequencing (WTSS), uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment in time.

A spliceosome is a large and complex molecular machine found primarily within the splicing speckles of the cell nucleus of eukaryotic cells.

(Not to be confused with mTORC1.) CREB-regulated transcription coactivator 1 (CRTC1), previously referred to as TORC1 (Transducer Of Regulated CREB activity 1), is a protein that in humans is encoded by the CRTC1 gene.

The genetic code is the set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins by living cells.

Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA (mRNA) by the enzyme RNA polymerase.

In genetics, a silencer is a DNA sequence capable of binding transcription regulation factors, called repressors.

The piwi (sometimes also PIWI; originally P-element Induced WImpy testis in Drosophila) class of genes was originally identified as encoding regulatory proteins responsible for maintaining incomplete differentiation in stem cells and maintaining the stability of cell division rates in germ line cells.

An intron is any nucleotide sequence within a gene that is removed by RNA splicing during maturation of the final RNA product.

RNA polymerase (RNAP or RNApol) (Ribonucleic acid), also known as DNA-dependent RNA polymerase, is an enzyme that produces primary transcript RNA.

In the genetic code, a stop codon (or termination codon) is a nucleotide triplet within messenger RNA that signals a termination of translation into proteins.

In genetics, an operon is a functioning unit of genomic DNA containing a cluster of genes under the control of a single promoter.

In molecular biology and genetics, a transcription factor (sometimes called a sequence-specific DNA-binding factor) is a protein that binds to specific DNA sequences, thereby controlling the rate of transcription of genetic information from DNA to messenger RNA.

Uridine-5'-triphosphate (UTP) is a pyrimidine Nucleoside triphosphate, consisting of the organic base uracil linked to the 1' carbon of the ribose sugar, and esterified with tri-phosphoric acid at the 5' position.

RNA interference (RNAi) is a biological process in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecules.

An exon is any part of a gene that will encode a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing.

The 5' untranslated region (5′ UTR) (also known as a Leader Sequence or Leader RNA) is the region of an mRNA that is directly upstream from the initiation codon.

In genetics, a promoter is a region of DNA that initiates transcription of a particular gene.

The retinoblastoma protein (protein name abbreviated pRb; gene name abbreviated RB or RB1) is a tumor suppressor protein that is dysfunctional in several major cancers.

A signal peptide (sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway.

Messenger RNA (mRNA) is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acid sequence of the protein products of gene expression.

A microRNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals and some viruses, that functions in RNA silencing and post-transcriptional regulation of gene expression.

A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface.

The B3 DNA binding domain (DBD) is a highly conserved domain found exclusively in transcription factors, from higher plants (≥40 species) (Pfam PF02362) combined with other domains (InterPro: IPR003340).

Most of the times, regulatory elements occur upstream of operons.

Anisomycin, also known as flagecidin, is an antibiotic produced by Streptomyces griseolus which inhibits eukaryotic protein synthesis.

S-adenosylmethionine synthetase (EC 2.5.1.6) (also known as methionine adenosyltransferase (MAT)) is an enzyme that creates S-adenosylmethionine (AdoMet) by reacting methionine (a non-polar amino acid) and ATP (the basic currency of energy).

Activating Protein 2 (AP-2) is a family of closely related transcription factors which plays a critical role in regulating gene expression during early development.

geWorkbench (genomics Workbench) is an open-source software platform for integrated genomic data analysis.

Nuclear receptor-interacting protein 1 (NRIP1) also known as receptor-interacting protein 140 (RIP140) is a protein that in humans is encoded by the NRIP1 gene.

GenePattern is a freely available computational biology open-source software package developed at the Broad Institute of MIT and Harvard for the analysis of genomic data.

YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48000 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references.

A working copy of the Intronerator no longer exists as of 2003.

Nucleic acid analogues are compounds which are analogous (structurally similar) to naturally occurring RNA and DNA, used in medicine and in molecular biology research.

Mouse Genome Informatics (MGI) is a free, online database and bioinformatics resource hosted by The Jackson Laboratory, with funding by The National Human Genome Research Institute (NHGRI), the National Cancer Institute (NCI) and the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD).

Transcription factor II Human (TFIIH) is one of several general transcription factors that make up the RNA polymerase II preinitiation complex.

Members of the signal transducer and activator of transcription (STAT) protein family are intracellular transcription factors that mediate many aspects of cellular immunity, proliferation, apoptosis and differentiation.

Transcription factor IIF (TFIIF) is one of several general transcription factors that make up the RNA polymerase II preinitiation complex.

Transcription factor TFIIA is a nuclear protein involved in the RNA polymerase II-dependent transcription of DNA.

Proline-, glutamic acid- and leucine-rich protein 1 (PELP1) also known as modulator of non-genomic activity of estrogen receptor (MNAR) and transcription factor HMX3 is a protein that in humans is encoded by the PELP1 gene.

A capping enzyme (CE) is an enzyme that catalyzes the attachment of the 5' cap to messenger RNA molecules that are in the process of being synthesized in the cell nucleus during the first stages of gene expression.

RNA-dependent RNA polymerase (RdRP), (RDR), or RNA replicase, is an enzyme that catalyzes the replication of RNA from an RNA template.

A sigma factor (σ factor) is a protein needed only for initiation of RNA synthesis.

Post-transcriptional regulation is the control of gene expression at the RNA level, therefore between the transcription and the translation of the gene.

Post-translational regulation refers to the control of the levels of active protein.

Signal transducer and activator of transcription 5 (STAT5) refers to two highly related proteins, STAT5A and STAT5B, which are part of the seven-membered STAT family of proteins.

Transcription factor II E (TFIIE) is one of several general transcription factors that make up the RNA polymerase II preinitiation complex.

In the field of molecular biology, the ETS (E26 transformation-specific or E-twenty-six) family is one of the largest families of transcription factors and is unique to metazoans.

(p)ppGpp, guanosine pentaphosphate or tetraphosphate is an alarmone which is involved in the stringent response in bacteria, causing the inhibition of RNA synthesis when there is a shortage of amino acids present.

In molecular biology and bioinformatics, SNP array is a type of DNA microarray which is used to detect polymorphisms within a population.

Effective is a database of predicted bacterial secreted proteins.

Interferome comprises the following data sets: * Gene expression data of interferon regulated genes from Homo sapiens, Mus musculus, and Pan troglodytes, manually curated from more than 30 public and inhouse microarray and proteomic datasets.

The scleraxis protein is a member of the basic helix-loop-helix (bHLH) superfamily of transcription factors.