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Table 7 Differentially expressed genes related to the UPS, as determined by SAM and LIMMA

From: Microarray analysis of peripheral blood lymphocytes from ALS patients and the SAFE detection of the KEGG ALS pathway

αProbe βSymbol γAccession δFC εFunctional Description
A_23_P317800 ANAPC4 NM_013367 1.40 anaphase promoting complex subunit 4: Component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C complex acts by mediating ubiquitination and subsequent degradation of target proteins: it mainly mediates the formation of 'Lys-11'-linked polyubiquitin chains and, to a lower extent, the formation of 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains
A_23_P106741 PSMD7 NM_002811 1.41 proteasome (prosome, macropain) 26S subunit, non-ATPase, 7: Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins
A_23_P120153 RNF149 NM_173647 1.67 E3 ubiquitin-protein ligase RNF149: Unknown
A_23_P42664 SHFM1 NM_006304 1.63 split hand/foot malformation (ectrodactyly) type 1: Subunit of the 26S proteasome which plays a role in ubiquitin-dependent proteolysis
A_24_P172481 TRIM22 NM_006074 1.55 E3 ubiquitin-protein ligase TRIM22: Interferon-induced antiviral protein involved in cell innate immunity. The antiviral activity could in part be mediated by TRIM22-dependent ubiquitination of viral proteins. Plays a role in restricting the replication of HIV-1, encephalomyocarditis virus (EMCV) and hepatitis B virus (HBV). Acts as a transcriptional repressor of HBV corepromoter. May have E3 ubiquitin-protein ligase activity.
A_23_P203137 UBE4A NM_004788 1.34 ubiquitin conjugation factor E4 A: Binds to the ubiquitin moieties of preformed conjugates and catalyzes ubiquitin chain assembly in conjunction with E1, E2, and E3.
A_23_P152066 UBR1 NM_174916 1.33 ubiquitin protein ligase E3 component n-recognin 1: E3 ubiquitin-protein ligase which is a component of the N-end rule pathway. Recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. Plays a critical role in chromatin inactivation and chromosome-wide transcriptional silencing during meiosis via ubiquitination of histone H2A. Binds leucine and is a negative regulator of the leucine-mTOR signaling pathway, thereby controlling cell growth.
A_23_P362637 UBR2 NM_015255 1.25 ubiquitin protein ligase E3 component n-recognin 2: Same as for UBR1
A_32_P178945 YOD1 NM_018566 1.52 YOD1 OTU deubiquinating enzyme 1 homolog alias HIV-1-induced protease: Hydrolase that can remove conjugated ubiquitin from proteins and participates in endoplasmic reticulum-associated degradation (ERAD) for misfolded lumenal proteins. May act by triming the ubiquitin chain on the associated substrate to facilitate their threading through the VCP/p97 pore. Ubiquitin moieties on substrates may present a steric impediment to the threading process when the substrate is transferred to the VCP pore and threaded through VCP's axial channel. Mediates deubiquitination of both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. Able to cleave both polyubiquitin and di-ubiquitin.
  1. A total of nine genes among 206 related to the ubiquitin/proteasome system (UPS) were significantly upregulated in lymphocytes from ALS patients compared to controls, as determined by SAM (q < 1%) and LIMMA analyses (p < 0.001). Among them, four genes encode E3 ubiquitin ligases (RNF149, TRIM22, UBR1, and UBR2) and one gene a deubiquitinase (YOD1). αAgilent Array 4 × 44K probe IDs, βgene symbol, γNCBI GenBank accession number, δfold change in expression and εGeneCard functional description (http://www.genecards.org) are provided.