Motif over-representation analysis with shuffled matrices
To assess the probability of a PWM's predictions being enriched within as many datasets as observed with the zinger PWMs, we shuffled the PFMs of the zingers and fit a distribution to the results.
Motif finder The Motif finder is used to find six base pair stretches (6-mers) that are over-represented within a given set of upstream sequences. It can be used to identify potential cis-regulatory sequences in a set of genes.
Motifs are simple combinations of secondary structure that occur in many different proteins and which carry out a similar function. An example is the helix-loop helix. It consists of two antiparallel helices at about a 60-degree angle to each other connected by a loop.
A common motif in the secondary structure of proteins, the alpha helix (α-helix) is a right-handed coiled conformation, resembling a spring, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier ( hydrogen bonding).
A protein binding motif that contain ~7 regions ~40 aa long containing a conserved W & D. Below is a picture of a WD40 region of Human Groucho/Tle1 (1GXR) from L. H. Pearl, S. M. Roe, L. M. Pickles.
side view ...
Leucine zipper: A motif found in certain proteins in which Leu residues are evenly spaced through an a-helical region, such that they would end up on the same face of the helix. Dimers can form between two such proteins.
Protein sequence analysis at UCL: Our research concerns protein sequence analysis, primarily exploiting the technique of protein `fingerprinting' (which uses conserved motifs to characterise particular folds and functionalities).
Helix-turn-helix motifs (← links)
Organelles (← links)
Starter trna (← links)
Eukaryote (← links)
Secretory protein (← links)
Archaea (← links)
Archaebacteria (← links)
Messenger rnas (← links)
Organelle (← links)
Chaperone (← links)
Chaperonin (← links) ...
Domains often contain smaller motifs, consisting of a conserved pattern of amino acids, or of combinations of structural elements formed by the folding of nearby amino acid sequences. An example of a motif is a helix-loop-helix, which binds to DNA.
Very high repetitions (from 1,000 to over 100,000 copies) of a basic motif or repeat unit (commonly 100 - 300 base pairs) which occur at a few loci on the genome.
Three-dimensional structure of gene product (protein) with known or implied function.
Homeobox. A DNA sequence motif found in the coding region of many regulatory genes; the encoded amino acid structure has a helix-loop-helix structure.
Homeotic (HOX) gene. Any of a group of genes in which mutation results in the replacement of one body structure by another body structure.
Autoregulatory loops: In this type of regulatory motif, a transcription factor binds to regulatory sequences that regulate its own transcription. Such interactions can be positive (amplifying) or negative (squelching).
where the subscripts indicate the number of residues present. The motif is named for the finger-like loop of amino acids that protrudes from the zinc binding site (known as the "Cys₂/His₂ finger" (pronounced "siss-two-hiss-two").
Sara O. Dionne1, Douglas F. Lake, William J. Grimes and Margaret H. Smith, Identification of HLA-Cw6.02 and -Cw7.01 allele-specific binding motifs by screening synthetic peptide libraries. Immunogenetics 56, 391-399 (2004).
A small portion of a gene or protein that appears in many genes or proteins that are related in structure; the box usually has some specific function, sometimes called a "motif", like binding DNA or interacting with specific proteins or other molecules.
Miniature Inverted-repeat Transposable Elements (MITEs)
The recent completion of the genome sequence of rice and C. elegans has revealed that their genomes contain thousands of copies of a recurring motif consisting of ...
In these molecules, the tetrahedral shape of carbon bonded to four other atoms is often a repeating motif.
Biological molecules recognize and interact with one another with a specificity based on molecular shape.