Overview of gene classes

Class Description Number of genes in class Genes in SilenceSelect Genes in FLeXSelect
Anti-apoptosis Proteins that directly inhibit any of the steps required for cell death by apoptosis 153 89 36
Apoptosis Signaling Proteins that participate in a process that directly activates any of the steps required for cell death by apoptosis 187 95 42
CD Molecules The cluster of differentiation (cluster of designation) are cell surface molecules present on leukocytes 347 254 96
Cell Adhesion Proteins Proteins involved in cell adhesion process 157 76 25
Cell Cycle Proteins Proteins involved in cell cycle processes 471 191 70
Cytochrome P450 Cytochrome P450 proteins (or CYPs) are primarily membrane-associated proteins, located either in the inner membrane of mitochondria or in the endoplasmic reticulum of cells. CYPs metabolize thousands of endogenous and exogenous compounds. 56 51 2
Cytokines Signaling molecules that are used extensively in cellular communication 208 207 57
This class of cytokines is characterized by small size (they are all approximately 8-10 kDa in size), and the presence of four cysteine residues in conserved locations that are key to forming their 3-dimensional shape 49 49 20
Hematopoietic growth factors (abbr. HGF) or Hematopoietic cytokines, which act on cells of the hematopoietic system 27 27 7
This class primarily includes IL-1 and IL-18 11 11 3
This class includes IL-10, IL-19, IL-20, IL-22, IL-24, IL-26 6 6 1
Cytokines of this class have a specific effect in promoting proliferation of T-cells that cause cytotoxic effects 5 5 1
Cell-signaling proteins produced by the cells of the immune system in response to challenges such as viruses, parasites and tumor cells 15 15 0
Platelet-derived growth factors (PDGFs) 9 9 5
Transforming growth factor beta family of cytokines 29 28 6
TNF-like cytokine class 19 19 4
DNA Repair Proteins Proteins involved in DNA repair 168 56 14
Enzymes Proteins that catalyze various biochemical reactions 3381 2336 591
Class of enzymes that catalyze the hydrolysis of a chemical bond 589 302 80
Class of enzymes catalyzing the structural rearrangement of isomers 90 43 11
Class of enzymes that can catalyse the joining of two large molecules by forming a new chemical bond, usually with accompanying hydrolysis of a small chemical group 165 78 11
Class of enzymes that cleave various chemical bonds by means other than hydrolysis and oxidation 93 42 6
Class of enzymes that catalyze oxidation/reduction reactions 420 264 33
Class of enzymes that remove a phosphate group from its substrate by hydrolysing phosphoric acid monoesters into a phosphate ion and a molecule with a free hydroxyl group 215 169 19
Class of enzymes that conducts proteolysis of peptide bonds. This class includes: Serine proteases, Threonine proteases, Cysteine proteases, Aspartate proteases, Metalloproteases and Glutamic acid proteases. 569 507 205
Class of enzymes that catalyze the transfer of a functional group (e.g. a methyl or phosphate group) from one molecule (called the donor) to another (called the acceptor). 1237 938 237
GPCR Ligand-sensing receptors that upon ligand binding activate an associated G-protein by exchanging its bound GDP for a GTP 752 384 236
Adenosine and Adenine Nucleotide Receptors 17 17 15
Adhesion-GPCRs have vital dual roles in cellular adhesion and signalling 32 32 9
Chemokine receptors are predicted to be a seven transmembrane domain proteins similar to G protein-coupled receptors 29 29 26
Members of the frizzled gene family encode 7-transmembrane domain proteins that are receptors for Wnt signaling proteins. Smoothened (Smo) receptors are non-classical G-protein-coupled receptors that belong to the Frizzled family. Smoothened receptors lack the ability to directly interact with their endogenous ligand, Hedgehog (Hh). 13 13 6
Lysophosphatidic acid (LPA) receptors from a group known as EDG receptors. These receptors are members of the G protein-coupled receptor superfamily 14 14 11
The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals 355 13 13
Group of light-sensitive 35-55 kDa membrane-bound G protein-coupled receptors of the retinylidene protein family found in photoreceptor cells of the retina 10 9 2
The secretin-like GPCRs include secretin, calcitonin, parathyroid hormone/parathyroid hormone-related peptides and vasoactive intestinal peptide receptors 47 47 14
The serotonin (5-hydroxytryptamine, 5-HT) receptors are a group of G protein-coupled receptors and ligand-gated ion channels found in the central and peripheral nervous system 12 12 8
Receptors that facilitate the sensation of taste 17 1 0
Ion Channels Ion channels are pore-forming proteins that help establish and control the small voltage gradient across the plasma membrane. 353 291 22
This class include among others chloride channels 58 49 8
Includes potassium, calcium, proton channels 296 250 18
Also known as ionotropic receptors, this group of channels open in response to specific ligand molecules binding to the extracellular domain of the receptor protein. 147 132 13
Class of proteins that are directly or indirectly involved in ion transport 28 16 3
Voltage-gated channels open and close in response to membrane potential. 159 131 4
Kinases Class of enzymes alternatively known as phosphotransferase that transfers phosphate groups from high-energy donor molecules, such as ATP, to specific substrates. Protein kinases transfer phosphate to a protein. 547 537 162
Includes the cyclic-nucleotide-dependent family (PKA and PKG), the protein kinase C family, the ?-adrenergic receptor kinase (?ARK), the ribosomal S6 family and other close relatives. These kinases have a strong preference for phosphorylation of Ser/Thr residues in close proximity to the basic amino acids Lysine and Arginine. 61 61 20
The Atypical kinases are a small set of protein kinases that do not share clear sequence similarity with other conventional kinases 25 25 1
Calcium/calmodulin-dependent protein kinases 70 70 21
Casein kinase family 12 12 4
Includes cyclin-dependent kinases (CDKs), mitogen-activated protein kinases (MAP kinases), glycogen synthase kinases (GSK) and CDK-like kinases 60 60 28
Similar to NIMA (never in mitosis A) kinases 11 11 3
The receptor guanylate cyclases are a small ePK group similar in sequence to the Tyrosine Kinase group 5 5 0
The STE group includes many protein kinases involved in MAP kinase cascades 54 54 16
Tyrosine kinase-like kinases are serine-threonine protein kinases named so because of their close sequence similarity to tyrosine kinases. 34 34 13
Tyrosin protein kinase family 91 90 24
NHR Nuclear hormone receptors class 48 48 27
Protease Inhibitors Proteins that inhibit proteases 21 21 6
Protease Substrates Class of proteins that are themselfves substrates for different proteases. Information relating to the specific residue requirements spanning the protease cleavage site in peptide substrates is often used in assisting the development of specific inhibitors and in identifying possible in vivo protein substrates. 326 229 95
Protein Phosphatases Specific class of phosphatases that remove a phosphate group from a protein. Their action is opposite to that of kinases. 170 144 19
Receptors General class of receptor proteins 1697 1021 397
Class of cell surface receptors that binds a signaling molecule in addition to a primary receptor in order to facilitate ligand recognition. 17 7 7
Class of ligand-dependent receptors found in the nucleus of the cell 59 55 28
Class of receptors activated by neurotransmitter ligands: The majority of neurotransmitter receptors are integral membrane proteins with seven transmembrane domains, commonly coupled to G-proteins. Binding of a ligand to its specific neurotransmitter receptor may result in the activation of a myriad of cell signal transduction pathways and modulation of ion channel homeostasis. 98 93 30
Proteins that are not similar to most common receptor classes 413 204 56
Pattern recognition receptors, or PRRs, are proteins expressed by cells of the innate immune system to identify pathogen-associated molecular patterns. They include the large families of membrane-bound Toll-like receptors, cytoplasmic NOD-like receptors and Endocytic PRRs. 12 9 1
A specific group of G protein-coupled receptors that respond to small peptides 114 108 71
Receptors modulated by Phorbol Esters. These receptors have been implicated in many cancer development studies and inflammatory responses. 11 11 2
Group of chromo-proteins that initiating a signal transduction cascade upon exposure to a certain wavelength of light 11 6 1
A large group of transmembrane receptors 1173 723 304
Scaffold Proteins Proteins that interact and/or bind with members of a signaling pathways, tethering them into complexes 38 21 5
Secreted/Extracellular Secreted and extracellular proteins 3669 1943 749
Extracellular matrix proteins 129 96 25
Senescence Proteins Proteins involved in senescence 6 2 3
Signal Transduction Proteins involved in signal transduction 2041 1347 511
Small molecule targets Genes that code proteins that are potentially druggable with small molecules 4565 3098 869
Structural Constituents of Cytoskeleton Proteins that contribute to the structural integrity of a cytoskeletal structure 67 16 3
Transcription Cofactors Proteins that link a sequence-specific transcription factor to the core RNA polymerase II complex but does not bind DNA itself. 300 110 42
Transcription Factors Contain DNA-binding domain (DBD), Trans-activating domain (TAD) and an optional signal sensing domain (SSD) (e.g., a ligand binding domain) 1360 255 117
Translation Regulators Proteins that are involved in positive or negative regulation of translation 69 11 2
Transporters Proteins that move substances, both uncharged and charged (ionic), across cell membranes 524 346 52
Proteins that in some way facilitate transport across one or more biological membranes but do not themselves participate directly in the transmembrane translocation of a substrate are included in this subclass. 34 16 4
Transporter proteins that utilize a carrier-mediated process to catalyze uniport (a single species is transported either by mediated diffusion or in a membrane-potential-dependent manner if the solute is charged), antiport (two or more species are transported in opposite directions in a tightly coupled process, not utilizing chemical free energy), or symport (two or more species are transported together in the same direction in a coupled process, again not utilizing any form of energy other than the electrochemical potential gradient). 46 24 4
Transporter proteins that use the free energy of P-P bond hydrolysis to drive the movement of substances against their chemical or electrochemical potential gradient as well as oxidoreduction-driven transporters 111 67 13
These transporters usually catalyze the movement of solutes by an energy-independent passage through a trans-membrane aqueous pore without evidence for a porter (i.e. carrier)-mediated mechanism. 160 108 24
Class of a few proteins which act as translocators of electrons across the membrane 9 5 1
Ubiquitination Proteins that participate in the process by which one or more ubiquitin moieties are added to a protein 93 66 9