| Description | Protein localization assemblies constructed from integrating AP-MS biomolecular interaction and IF imaging data |
| Measurement | association by data aggregation |
| Association | protein-biological term associations from integrated AP-MS interactions and IF imaging |
| Category | structural or functional annotations |
| Resource | Cell Maps for AI |
| Citation(s) | |
| Last Updated | 2025 Sep 29 |
| Stats |
|
| API | |
| Script | |
| Downloads |
Gene Attribute
Gene Similarity
Attribute Similarity
UMAP
271 sets of proteins comprising assemblies from integrated AP-MS and IF data from the CM4AI U2OS Cell Map Protein Localization Assemblies dataset.
| Gene Set | Description |
|---|---|
| Mitochondrion | A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. |
| No annotation - 1 | |
| Nucleoli | |
| Nuclear speckles | |
| Plasma membrane | The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. |
| Cytoskeleton organization and intracellular signaling | |
| Cellular metabolism and vesicular transport regulation | |
| Intracellular signaling and cell migration supercomplex | |
| Chromatin factors | |
| Golgi apparatus | A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. |
| Intracellular protein transport and DNA repair | |
| Nuclear splicing speckle | |
| Preribosome | Any complex of pre-rRNAs, ribosomal proteins, and associated proteins formed during ribosome biogenesis. |
| Extracellular matrix organization and signaling modulation | |
| No annotation - 2 | |
| Intracellular signaling and cytoskeletal dynamics | |
| Microtubules | |
| Nuclear pore complex and nucleocytoplasmic transport | |
| No annotation - 3 | |
| No annotation - 4 | |
| Endoplasmic reticulum | The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). |
| Chromatin modification and transcriptional regulation 1 | |
| No annotation - 5 | |
| RNA polymerase and mediator super assembly | |
| Chromatin organization and gene expression regulators | |
| No annotation - 6 | |
| mRNA regulation complex | |
| Mitochondrial ribosome | A ribosome found in the mitochondrion of a eukaryotic cell; contains a characteristic set of proteins distinct from those of cytosolic ribosomes. |
| No annotation - 7 | |
| Nuclear speckle spliceosome subcomplex | |
| Chaperone-mediated protein folding complex | |
| SWI/SNF and transcription regulator | |
| Chromosome segregation and DNA repair | |
| Nucleoli fibrillar center | |
| Endocytic and cytoskeletal regulation | |
| Protein quality control and ubiquitin-proteasome system regulation | |
| Nuclear envelope and nucleocytoplasmic transport | |
| Pre-mRNA splicing and ribonucleoprotein assembly | |
| DNA replication and repair system | |
| Actin filaments | |
| Cytoskeletal dynamics and intracellular transport | |
| Proteasome-associated machinery | |
| Centrosome | A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle. |
| Cell cycle and division regulation | |
| Cytoplasmic vescicle for mRNA regulation | |
| No annotation - 8 | |
| No annotation - 9 | |
| Ubiquitin-proteasome complex | |
| Transcription regulators and chromatin remodelers | |
| Ribosome biogenesis complex | |
| Protein folding and complex assembly regulation | |
| No annotation - 10 | |
| Cytoskeletal organization and intracellular transport regulation | |
| Intermediate filaments | |
| Endosomal sorting and trafficking | |
| Actin cytoskeleton remodeling and signal transduction 1 | |
| Endosomal organization and transportation assembly 1 | |
| Mitochondrial large ribosomal subunit - 2 | |
| Anaphase-promoting and cell cycle kinase complexes | |
| RNA polymerase assembly | |
| No annotation - 11 | |
| Intracellular trafficking and peroxisomes | |
| Intracellular transport and vesicle-mediated processes | |
| NCOR-associated transcriptional regulation (NATR) | |
| DNA repair and telomere maintenance complex | |
| Mediator complex | A protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The mediator complex is required for activation of transcription of most protein-coding genes, but can also act as a transcriptional corepressor. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins. |
| Mitochondrial electron transport chain function | |
| Chromosome stability and DNA repair mechanisms | |
| SWI/SNF complex | A SWI/SNF-type complex that contains nine or more proteins, including both conserved (core) and nonconserved components; the Swi2/Snf2 ATPase is one of the core components. |
| Cytoskeletal organization and cell adhesion dynamics | |
| Endocytic regulation via ubiquitination 1 | |
| Cytosolic protein folding 1 | |
| Regulation of cell cycle and gene expression | |
| Endosomal organization and transportation assembly 2 | |
| Protein quality control and DNA repair | |
| Mitochondrial small ribosomal subunit | The smaller of the two subunits of a mitochondrial ribosome. |
| RNA metabolism and nuclear transport regulation | |
| Chromatin modification and transcriptional regulation 2 | |
| Cell junctions | |
| Proteasome complex | A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core. |
| P-body | |
| No annotation - 12 | |
| SAGA complex - 2 | |
| DNA damage repair and response system | |
| Cytosolic protein folding 2 | |
| Mitochondrial biogenesis and protein quality control | |
| RYBP/YAF2-PRC1 complexes in cell division | |
| Regulation of gene expression and mRNA processing - 2 | |
| Regulation of gene expression and cell cycle progression | |
| Endocytic pathway regulation and vesicle trafficking | |
| Cytochrome complex | A protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions. |
| Ras family interactors | |
| TFIIH transcription factor complex | |
| Regulation of gene expression and signal transduction | |
| Mitochondrial function and apoptosis regulation | |
| Protein folding and stress response regulation | |
| Endocytosis complex | |
| Zinc finger transcription factors | |
| Endocytic regulation via ubiquitination 2 | |
| Mitocondrial and membrane associated processing | |
| Collagen biosynthesis and extracellular matrix organization | |
| Lysosomal function and lipid metabolism | |
| NSL-MLL complex | |
| RNAse mitochondrial RNA processing (MRP) complex | |
| No annotation - 13 | |
| Large ribosomal subunit | The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). |
| NuA4 histone acetyltransferase complex | A complex having histone acetylase activity on chromatin, as well as ATPase, DNA helicase and structural DNA binding activities. The complex is thought to be involved in double-strand DNA break repair. Subunits of the human complex include HTATIP/TIP60, TRRAP, RUVBL1, BUVBL2, beta-actin and BAF53/ACTL6A. In yeast, the complex has 13 subunits, including the catalytic subunit Esa1 (homologous to human Tip60). |
| proton-transporting V-type ATPase complex | A proton-transporting two-sector ATPase complex that couples ATP hydrolysis to the transport of protons across a concentration gradient. The resulting transmembrane electrochemical potential of H+ is used to drive a variety of (i) secondary active transport systems via H+-dependent symporters and antiporters and (ii) channel-mediated transport systems. The complex comprises a membrane sector (V0) that carries out proton transport and a cytoplasmic compartment sector (V1) that catalyzes ATP hydrolysis. V-type ATPases are found in the membranes of organelles such as vacuoles, endosomes, and lysosomes, and in the plasma membrane. |
| Mitotic cell cycle progression and regulation 1 | |
| AP-1 transcription factor complex | |
| No annotation - 14 | |
| Regulation of cellular architecture and autophagy | |
| Intracellular trafficking and lipid signaling regulation | |
| Mitochondrial function and metabolism regulation | |
| Ribosome biogenesis and RNA processing | |
| Nonhomologous end joining repair complex | |
| Chromatin remodeling and transcriptional regulation 1 | |
| Collagen biosynthesis | |
| Regulation of gene expression and mRNA processing | |
| Protocadherin-mediated cell adhesion and signaling | |
| Regulation of gene expression and protein quality control | |
| No annotation - 15 | |
| Regulation of gene expression and protein modification | |
| Amyloid precursor protein complex 1 | |
| Mitotic cell cycle progression and regulation 2 | |
| 9-1-1-RAD17-RFC complex | |
| Rag-Ragulator complex | |
| SAGA complex | A SAGA-type histone acetyltransferase complex that contains Spt8 (in budding yeast) or a homolog thereof; additional polypeptides include Spt group, consisting of Spt7, Spt3, and Spt20/Ada5, which interact with the TATA-binding protein (TBP); the Ada group, consisting of Ada1, Ada2, Ada3, Ada4/Gcn5, and Ada5/Spt20, which is functionally linked to the nucleosomal HAT activity; Tra1, an ATM/PI-3 kinase-related protein that targets DNA-bound activators for recruitment to promoters; the TBP-associated factor (TAF) proteins, consisting of Taf5, Taf6, Taf9, Taf10, and Taf12, which mediate nucleosomal HAT activity and are thought to help recruit the basal transcription machinery. |
| Energy metabolism regulation complex | |
| Heat shock protein complex | |
| Intracellular trafficking and signal transduction modulation | |
| Protein processing and intracellular signaling | |
| mRNA surveillance and decay pathway | |
| Pre-mRNA splicing and snRNA processing | |
| SCF ubiquitin ligase complex | A ubiquitin ligase complex in which a cullin from the Cul1 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a Skp1 adaptor and an F-box protein. SCF complexes are involved in targeting proteins for degradation by the proteasome. The best characterized complexes are those from yeast and mammals (with core subunits named Cdc53/Cul1, Rbx1/Hrt1/Roc1). |
| RNA polymerase III | |
| Mitotic cell cycle and chromosome segregation regulators | |
| Transcriptional regulation and signal transduction | |
| Aminoacyl-tRNA synthetase multienzyme assembly | |
| CENP-H-I complex | |
| SNARE complex | A protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers. One well-characterized example is the neuronal SNARE complex formed of synaptobrevin 2, syntaxin 1a, and SNAP-25. |
| Protein quality control and DNA repair complex | |
| Vesicle trafficking and regulation 1 | |
| Hematopoietic regulation and bone development | |
| RNA polymerase II | |
| PRC1 complex | A multiprotein complex that mediates monoubiquitination of lysine residues of histone H2A (lysine-118 in Drosophila or lysine-119 in mammals). The complex is required for stable long-term maintenance of transcriptionally repressed states and is involved in chromatin remodeling. |
| Nuclear transport and gene expression regulation | |
| Regulation of mRNA processing and protein ubiquitination | |
| Ciliary assembly | |
| Signal recognition particle (SRP) associated protein translocation | |
| Mitochondrial Function and Regulation | |
| RNA processors | |
| GID complex | A protein complex with ubiquitin ligase activity that is involved in proteasomal degradation of fructose-1,6-bisphosphatase (FBPase) and phosphoenolpyruvate carboxykinase during the transition from gluconeogenic to glycolytic growth conditions. In S. cerevisiae, the GID (Glucose Induced degradation Deficient) complex consists of Vid30p, Rmd5p, Vid24p, Vid28p, Gid7p, Gid8p, and Fyv10p. |
| No annotation - 16 | |
| BLOC-1 complex | A protein complex required for the biogenesis of specialized organelles of the endosomal-lysosomal system, such as melanosomes and platelet dense granules. Many of the protein subunits are conserved between mouse and human; the mouse complex contains the Pallidin, Muted, Cappuccino, Dysbindin, Snapin, BLOS1, BLOS2, AND BLOS3 proteins. |
| No annotation - 17 | |
| Clathrin-mediated endocytosis | An endocytosis process that begins when material is taken up into clathrin-coated pits, which then pinch off to form clathrin-coated endocytic vesicles. |
| Septin complex 1 | |
| NELF complex | A complex of five proteins, designated NELF-A, -B, -C, -D, and -E in human, that can physically associate with RNP polymerase II to induce transcriptional pausing. |
| No annotation - 18 | |
| G-protein signaling and cell cycle regulation | |
| Regulation of gene expression and signal transduction in immune and stress responses | |
| eIF3 complex 1 | |
| RNA polymerase II transcriptional regulation and mRNA processing | |
| Ubiquitin-mediated cell cycle regulation | |
| tRNA splicing endonuclease and telomere cap assembly | |
| Mitochondrial metabolism and protein regulation | |
| Mitochondrial large ribosomal subunit | The larger of the two subunits of a mitochondrial ribosome. Two sites on the ribosomal large subunit are involved in translation: the aminoacyl site (A site) and peptidyl site (P site). |
| Regulation of Cellular Signaling and Transcription | |
| Mitotic spindle assembly and cell cycle regulation | |
| Chromatin remodeling and transcriptional regulation 2 | |
| Transcription factor TFTC complex | A protein complex that does not contain either a TATA-binding protein (TBP) or a TBP-like factor, but is composed of several TAFIIs and other proteins, including a histone acetyltransferase. This complex is able to nucleate transcription initiation by RNA polymerase II, can mediate transcriptional activation, and has histone acetyltransferase activity. |
| Extracellular matrix organization subcomplex | |
| Regulation of apoptosis and RNA modification | |
| Regulation of gene expression and chromatin remodeling | |
| Golgi apparatus organization and signaling | |
| Potential Ciliary Function and Assembly | |
| Amyloid precursor protein complex 2 | |
| Regulation of gene expression and cellular stress response | |
| Septin complex 2 | |
| No annotation - 19 | |
| Immune response modulation and cellular differentiation signaling | |
| Nucleocytoplasmic transport and post-transcriptional regulation | |
| Chromatin-associated cell division complexes | |
| Neurotransmitter Regulation and Iron Homeostasis | |
| Nuclear transcription regulators | |
| No annotation - 20 | |
| MAPK signaling pathway | |
| eIF3 complex 2 | |
| Regulation of mRNA translation and cellular metabolism | |
| Mitochondrial metabolic enzymes | |
| Chromatin organization and methylation cycle maintenance | |
| CST complex | |
| NSL complex | A histone acetyltransferase complex that catalyzes the acetylation of a histone H4 lysine residues at several positions. In human, it contains the catalytic subunit MOF, NSL1/KIAA1267, NSL2/KANSL2, NSL3/KANSL3, MCRS1, PHF20, OGT1, WDR5 and HCF1. |
| R2TP complex | A highly conserved protein complex comprised of two ATP-dependent DNA helicases (Rvb1p and Rvb2p in yeast, Pontin52 and Reptin52 in humans), Pih1p in yeast or PIH1D1 in humans, and Tah1 in yeast or RPAP3 in humans. The complex associates with Hsp90 and is thought to have a role in assembly of large protein or protein/nucleic acid complexes. In this role it is involved in multiple processes such as box C/D snoRNP biogenesis, phosphatidylinositol-3 kinase-related protein kinase (PIKK) signaling, RNA polymerase II assembly, and others. |
| snRNP assembly | |
| mRNA regulation and decay | |
| STRIPAK complex | |
| Transcription Factor IID complex (TFIID) | |
| Proteasome assembly and regulation | |
| GNAS-L-GNB4-GNG2 complex | |
| Mitochondrial aminoacyl-tRNA synthesis and branched-chain amino acid catabolism | |
| Notch signaling | |
| Mitochondrial dynamics and metabolism | |
| Regulation of circadian rhythm and response to hypoxia | |
| Endoplasmic reticulum morphology and vesicular traffic regulation | |
| No annotation - 21 | |
| Regulation of gene expression and chromosomal stability | |
| No annotation - 22 | |
| IkappaB kinase complex | A trimeric protein complex that phosphorylates inhibitory-kappaB (I-kappaB) proteins. The complex is composed of two kinase subunits (alpha and beta) and a regulatory gamma subunit (also called NEMO). In a resting state, NF-kappaB dimers are bound to inhibitory IKB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription. |
| Vesicle trafficking and regulation 2 | |
| Regulation of cellular redox state and amino acid transport | |
| Regulation of cell cycle and transcription in development | |
| Actin cytoskeleton remodeling and signal transduction 2 | |
| Mitochondrial Integrity and Metabolism | |
| Hematopoietic Cell Differentiation and Function | |
| No annotation - 23 | |
| No annotation - 24 | |
| Chromatin organization and transcription initiation | |
| No annotation - 25 | |
| No annotation - 26 | |
| No annotation - 27 | |
| Intracellular trafficking and cytoskeletal organization | |
| Mitochondrial small ribosomal subunit transport core | |
| Ubiquitin-mediated proteolysis | |
| Regulation of Mitochondrial Translation and Cellular Signaling | |
| Regulation of Gene Expression and Nuclear Transport | |
| Regulation of Ribosome Biogenesis and RNA Processing | |
| Regulation of Gene Expression and Protein Ubiquitination | |
| Syntaxin-binding protein complex | |
| No annotation - 28 | |
| Septin mediated cytoskeleton organization | |
| Cellular Redox Homeostasis and Vesicular Trafficking | |
| Regulation of Cytoskeletal Dynamics and Cell Morphology | |
| Regulation of Cytoskeletal Dynamics and Gene Expression | |
| Protein Stability and Turnover Regulation | |
| Cellular Ion Homeostasis and Metal Ion Transport | |
| tRNA-splicing ligase complex | A protein complex that catalyzes the ligation of cleaved pre-tRNAs by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester. |
| mRNA cleavage and polyadenylation specificity factor complex | A multisubunit complex that binds to the canonical AAUAAA hexamer and to U-rich upstream sequence elements on the pre-mRNA, thereby stimulating the otherwise weakly active and nonspecific polymerase to elongate efficiently RNAs containing a poly(A) signal. |
| Microvesicular body biogenesis | |
| No annotation - 29 | |
| DPYSL complex | |
| mRNA Processing and Spliceosome Assembly | |
| No annotation - 30 | |
| Telomere maintenance and DNA repair | |
| THO complex and transcription export | |
| Glycogen synthase kinase-3 (gsk-3) signaling regulation | |
| No annotation - 31 | |
| Regulation of cellular stress responses and metal ion homeostasis | |
| No annotation - 32 | |
| mRNA Surveillance and Repair Pathway | |
| Regulation of hematopoiesis and bone development | |
| Arp2/3 protein complex | A stable protein complex that contains two actin-related proteins, Arp2 and Arp3, and five novel proteins (ARPC1-5), and functions in the nucleation of branched actin filaments. |
| No annotation - 33 | |
| Regulation of p53-mediated cellular stress response | |
| DNA Repair and Cellular Stress Response | |
| tRNA protein synthesis complex | |
| Ragulator complex subunit | |
| Exosome | |
| Stress response complex | |
| Cellular redox homeostasis and nucleotide biosynthesis regulation | |
| cAMP-dependent protein kinase signaling | |
| Nucleotide-activated protein kinase complex | |
| Interferon-stimulated gene factor 3 (ISGF3) complex | |
| TOM complex, mitochondrial | |
| No annotation - 34 | |
| No annotation - 35 | |
| Glycogen Metabolism and Autophagy Regulation | |
| No annotation - 36 | |
| Steroidogenesis and lipid metabolism | |
| DNA repair and transcriptional regulation |
