VCPIP1 Data Analysis

HGNC Gene Name
valosin containing protein interacting protein 1
HGNC Gene Symbol
VCPIP1
Identifiers
hgnc:30897 NCBIGene:80124 uniprot:Q96JH7
Orthologs
mgi:1917925 rgd:708520
INDRA Statements
deubiquitinations all statements
Pathway Commons
Search for VCPIP1
Number of Papers
19 retrieved on 2022-05-22

DepMap Analysis

The Dependency Map (DepMap) is a genome-wide pooled CRISPR-Cas9 knockout proliferation screen conducted in more than 700 cancer cell lines spanning many different tumor lineages. Each cell line in the DepMap contains a unique barcode, and each gene knockout is assigned a “dependency score” on a per cell-line basis which quantifies the rate of CRISPR-Cas9 guide drop. It has been found that proteins with similar DepMap scores across cell lines, a phenomenon known as co-dependent genes, have closely related biological functions. This can include activity in the same or parallel pathways or membership in the same protein complex or the same pathway.

We identified the strongest seven co-dependent genes (“Symbol”) for DUBs and ran GO enrichment analysis. We used Biogrid, IntAct, and Pathway Commons PPIDs, and the NURSA protein-protein interaction databases (PPIDs) to determine whether co-dependent genes interact with one another. The “Evidence” column contains the PPIDs in which the interaction appears as well as whether there is support for the association by an INDRA statement. As another approach to identify potential interactors, we looked at proteomics data from the Broad Institute's Cancer Cell Line Encyclopedia (CCLE) for proteins whose expression across ~375 cell lines strongly correlated with the abundance of each DUB; it has previously been observed that proteins in the same complex are frequently significantly co-expressed. The correlations and associated p-values in the CCLE proteomics dataset are provided. And, we determined whether co-dependent genes yield similar transcriptomic signatures in the Broad Institute's Connectivity Map (CMap). A CMap score greater than 90 is considered significantly similar.

DepMap Correlations

Symbol Name DepMap Correlation Evidence CCLE Correlation CCLE Z-score CCLE p-value (adj) CCLE Significant CMAP Score CMAP Type
HUWE1 HECT, UBA and WWE domain containing E3 ubiquitin protein ligase 1 0.415 IntAct INDRA (1) 0.45 2.37 4.57e-18
C16orf72 chromosome 16 open reading frame 72 0.331 -0.08 -0.53 5.24e-01
C8orf44 chromosome 8 open reading frame 44 0.223
OTUD5 OTU deubiquitinase 5 0.217 Reactome (4) 0.00 -0.07 9.64e-01
PPP2R5C protein phosphatase 2 regulatory subunit B'gamma 0.215 0.18 0.88 5.23e-02
POM121 POM121 transmembrane nucleoporin 0.21 Reactome (2) -0.23 -1.38 2.81e-05
TP53 tumor protein p53 -0.206 Reactome (4) 0.02 0.02 7.99e-01

Dependency GO Term Enrichment

Gene set enrichment analysis was done on the genes correlated with VCPIP1using the terms from Gene Ontology and gene sets derived from the Gene Ontology Annotations database via MSigDB.

Using the biological processes and other Gene Ontology terms from well characterized DUBs as a positive control, several gene set enrichment analyses were considered. Threshold-less methods like GSEA had relatively poor results. Over-representation analysis with a threshold of of the top 7 highest absolute value Dependency Map correlations yielded the best results and is reported below.

GO Identifier GO Name GO Type p-value p-value (adj.) q-value
GO:0006284 base-excision repair Biological Process 4.76e-05 1.48e-02 4.13e-03
GO:1903749 positive regulation of establishment of protein localization to mitochondrion Biological Process 9.13e-05 2.83e-02 4.13e-03
GO:1903747 regulation of establishment of protein localization to mitochondrion Biological Process 1.41e-04 4.37e-02 4.25e-03

Literature Mining

INDRA was used to automatically assemble known mechanisms related to VCPIP1 from literature and knowledge bases. The first section shows only DUB activity and the second shows all other results.

Deubiquitinase Activity

psp cbn pc bel_lc signor biogrid lincs_drug tas hprd trrust ctd vhn pe drugbank omnipath conib crog dgi | rlimsp isi tees geneways eidos trips medscan sparser reach
VCPIP1 deubiquitinates SPRTN. 9 / 9
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Of note, while this study was under consideration, it was proposed that SPRTN is deubiquitylated by VCPIP1.

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These observations show that depletion of USP11 and VCPIP1 inhibits SPRTN deubiquitination, but in contrast to previous reports, monoubiquitination does not restrict SPRTN access to chromatin.

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Upon formaldehyde treatment and other yet to be identified signals, SPRTN is deubiquitinated by USP11 (this study), USP7, and VCPIP1.

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Upon DPC induction, ATM and ATR kinase activates VCPIP1 and VCIP135 deubiquitinase, which in turn deubiquitinates SPRTN, regulating its chromatin localization.

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Neither VCPIP1 nor USP11 induce SPRTN deubiquitylation when overexpressed, while USP7 does (XREF_SUPPLEMENTARY).

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However, we observe that lack of SPRTN deubiquitination by USP11 and VCPIP1 did not affect recruitment on chromatin.

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VCPIP1, in turn, deubiquitinates SPRTN and promotes its chromatin relocalization.

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A previous study showed that VCPIP1 deubiquitinates SPRTN, promoting SPRTN localization to chromatin.

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We observed reduced SPRTN auto-cleavage upon DPC induction in USP11 and USP7 single and double-knockdown cells, suggesting that in the absence of USP11 and USP7, SPRTN could be deubiquitinated by VCPIP1, which is recruited to chromatin upon DPC induction.
VCPIP1 deubiquitinates SNTG2. 9 / 9
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One possible explanation, as described in our model (XREF_FIG), is that monoubiquitination of Syn5 occurs only transiently in early mitosis and is quickly reversed by the deubiquitinase VCIP135 in late mitosis.

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These results suggest that Syn5 is deubiquitinated by VCIP135.

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In late mitosis, the DUB VCIP135, which associates with p97 via its UBX-L (UBX like) domain, deubiquitinates Syn5, which permits interaction between the SNAREs, membrane fusion and finally the formation of Golgi cisternae [XREF_BIBR].

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Therefore, we determined whether Syn5 is deubiquitinated by VCIP135.

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Taken together, these results demonstrate that Syn5 is deubiquitinated by VCIP135 in late mitosis.Syn5 contains 17 lysines that are conserved between rat and human.

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One possible explanation, as described in our model, is that monoubiquitination of Syn5 occurs only transiently in early mitosis and is quickly reversed by the deubiquitinase VCIP135 in late mitosis.

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Syn5 is monoubiquitinated by the ubiquitin ligase HACE1 in early mitosis and deubiquitinated by the deubiquitinase VCIP135 in late mitosis.

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Taken together, these results demonstrate that Syn5 is deubiquitinated by VCIP135 in late mitosis.

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Syn5 is monoubiquitinated by the ubiquitin ligase HACE1 in early mitosis and deubiquitinated by the deubiquitinase VCIP135 in late mitosis.
VCPIP1 deubiquitinates STX5. 2 / 2
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Syntaxin 5 is monoubiquitinated by HACE1 in early mitosis and deubiquitinated by the de-ubiquitinase VCIP135 in late mitosis (Wang et al. 2004).

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Syntaxin 5 is monoubiquitinated by HACE1 in early mitosis and deubiquitinated by the de-ubiquitinase VCIP135 in late mitosis.

Other Statements

psp cbn pc bel_lc signor biogrid lincs_drug tas hprd trrust ctd vhn pe drugbank omnipath conib crog dgi | rlimsp isi tees geneways eidos trips medscan sparser reach
VCPIP1 affects VCP
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VCPIP1 activates VCP.
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VCPIP1 activates VCP. 4 / 4
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Next, we wanted to ascertain whether VCIP135 contributes to p97 and p47 mediated membrane fusion using an in vitro Golgi reassembly assay.

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Considering that the disassembly of the p97, p47, and SNARE complex by VCIP135 requires ATP hydrolysis (XREF_FIG E), we suggest that the function of VCIP135 in membrane fusion is to mediate the dissociation of the p97, p47, and SNARE complex, which may be part of the SNARE priming process.

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The deubiquitinase VCIP135, which is associated with the p97 and p47 complex, removes the ubiquitin moiety and thus allows p97 and p47 to fuse the membranes after mitosis (XREF_FIG) 37.

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As shown in XREF_FIG G, VCIP135 partially prevented alpha-SNAP binding to GST-syn5DeltaTM, suggesting that VCIP135 directs syntaxin5 to p97 and p47 but not to alpha-SNAP and NSF.
VCPIP1 inhibits VCP.
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VCPIP1 inhibits VCP. 3 / 3
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During mitosis, Cdk1 phosphorylates p47, p37 and VCIP135, and blocks p97 controlled membrane-fusion processes so that the Golgi membranes remain disassembled.

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Our in vitro Golgi reassembly assay confirmed that VCIP135 phosphorylation at S130 attenuates p97 and p47 mediated Golgi membrane fusion (XREF_FIG).

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In the presence of ATP, the addition of VCIP135 prevented p97 and p47 from binding to syntaxin5 and VCIP135 itself only bound poorly to syntaxin5 (XREF_FIG D, left three lanes).
VCPIP1 affects NSFL1C
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VCPIP1 activates NSFL1C.
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VCPIP1 activates NSFL1C. 3 / 3
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The deubiquitinase VCIP135, which is associated with the p97 and p47 complex, removes the ubiquitin moiety and thus allows p97 and p47 to fuse the membranes after mitosis (XREF_FIG) 37.

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Next, we wanted to ascertain whether VCIP135 contributes to p97 and p47 mediated membrane fusion using an in vitro Golgi reassembly assay.

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As shown in XREF_FIG G, VCIP135 partially prevented alpha-SNAP binding to GST-syn5DeltaTM, suggesting that VCIP135 directs syntaxin5 to p97 and p47 but not to alpha-SNAP and NSF.
VCPIP1 inhibits NSFL1C.
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In the presence of ATP, the addition of VCIP135 prevented p97 and p47 from binding to syntaxin5 and VCIP135 itself only bound poorly to syntaxin5 (XREF_FIG D, left three lanes).

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Our in vitro Golgi reassembly assay confirmed that VCIP135 phosphorylation at S130 attenuates p97 and p47 mediated Golgi membrane fusion (XREF_FIG).
VCPIP1 affects SNTG2
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VCPIP1 activates SNTG2. 4 / 4
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To investigate whether ubiquitinated Syn5 is a direct substrate of VCIP135, in vitro ubiquitinated Syn5 was treated with recombinant VCIP135.

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In late mitosis, VCIP135 is reactivated by dephosphorylation, removes ubiquitin from Syn5, and allows Syn5 interacting with its cognate SNARE Bet1 for membrane fusion at mitotic exit (XREF_FIG, right panel).

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In late mitosis, VCIP135 is reactivated by dephosphorylation, removes ubiquitin from Syn5, and allows Syn5 to interact with its cognate SNARE Bet1 for membrane fusion at mitotic exit.

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To investigate whether ubiquitinated Syn5 is a direct substrate of VCIP135, in vitro ubiquitinated Syn5 was treated with recombinant VCIP135 (Zhang and Wang, 2015; Zhang et al., 2014).
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Bisphenol A increases the amount of VCPIP1. 3 / 3
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VCPIP1 affects sub
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VCPIP1 inhibits sub.
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VCPIP1 inhibits sub. 2 / 2
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Taken together, our results demonstrate that phosphorylation of VCIP135 on S130 in early mitosis inactivates its DUB activity for mitotic Golgi disassembly; dephosphorylation in telophase reactivates VCIP135 to promote p97 and p47 mediated postmitotic Golgi membrane fusion.

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In this study, we found that phosphorylation of VCIP135 at a single site, S130, is necessary and sufficient to inactivate its DUB activity for Golgi disassembly in early mitosis.
VCPIP1 activates sub.
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VCPIP1 activates sub. 1 / 1
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Dephosphorylation of S130 on VCIP135 upon staurosporine or roscovitine but not U0126 treatment also significantly increased the DUB activity of endogenous VCIP135 (XREF_FIG), consistent with the hypothesis that phosphorylation at S130 inactivates VCIP135.
Succimer affects VCPIP1
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Succimer decreases the amount of VCPIP1. 2 / 2
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Magnetite nanoparticle decreases the amount of VCPIP1. 2 / 2
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VCPIP1 affects Ubiquitin
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As shown in Figure 3 A (lanes 3 and 4 versus lane 2), co-expression of WT VCIP135, but not the C218S mutant, significantly reduced the ubiquitin signal.

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As shown in XREF_FIG (lanes 3 and 4 vs. 2), co-expression of WT VCIP135, but not the C218S mutant, significantly reduced the ubiquitin signal (XREF_FIG).
VCPIP1 affects STX5
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VCPIP1 activates STX5. 2 / 2
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As shown in XREF_FIG G, VCIP135 partially prevented alpha-SNAP binding to GST-syn5DeltaTM, suggesting that VCIP135 directs syntaxin5 to p97 and p47 but not to alpha-SNAP and NSF.

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In mitosis, VCIP135 is phosphorylated at S130 by Cdk1 and thus is inactivated, allowing syntaxin 5 to be ubiquitinated by HACE1; in telophase, VCIP135 is dephosphorylated and reactivated, removing ubiquitin from syntaxin 5 to allow p97 mediated membrane fusion.

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In mitosis , VCIP135 is phosphorylated at S130 by Cdk1 and thus is inactivated , allowing syntaxin 5 to be ubiquitinated by HACE1 ; in telophase , VCIP135 is dephosphorylated and reactivated , removing ubiquitin from syntaxin 5 to allow p97-mediated membrane fusion Wang 2008 ) .

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In mitosis , VCIP135 is phosphorylated at S130 by Cdk1 and thus is inactivated , allowing syntaxin 5 to be ubiquitinated by HACE1 ; in telophase , VCIP135 is dephosphorylated and reactivated , removing ubiquitin from syntaxin 5 to allow p97-mediated membrane fusion ( Huang and Wang 2017 ; Wang 2008 ) .
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Therefore, monoubiquitinated syntaxin 5 recruits p97/p47 to the mitotic Golgi fragments and promotes post-mitotic Golgi reassembly upon ubiquitin removal by VCIP135 .

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Therefore, monoubiquitinated syntaxin 5 recruits p97/p47 to the mitotic Golgi fragments and promotes post-mitotic Golgi reassembly upon ubiquitin removal by VCIP135 (Huang et al. 2016).
VCPIP1 affects VCPIP1
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VCPIP1 bound to STX5 activates VCPIP1. 1 / 1
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The binding of VCIP135 to syntaxin5 independently of p47 (XREF_FIG C) allows VCIP135 to be closely associated with the p97 and p47 complex, whereas in cytosol such an association is less likely.
VCPIP1 activates VCPIP1. 1 / 1
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Dephosphorylation of S130 on VCIP135 upon staurosporine or roscovitine but not U0126 treatment also significantly increased the DUB activity of endogenous VCIP135 (XREF_FIG), consistent with the hypothesis that phosphorylation at S130 inactivates VCIP135.
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Venlafaxine increases the amount of VCPIP1. 1 / 1
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Valproic acid decreases the amount of VCPIP1. 1 / 1
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Urethane affects VCPIP1
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Urethane increases the amount of VCPIP1. 1 / 1
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Tunicamycin increases the amount of VCPIP1. 1 / 1
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Sodium arsenate increases the amount of VCPIP1. 1 / 1
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To our knowledge, the inhibition of VCPIP1 by PEITC is the first report of inhibition of an OTU domain DUB.
Phenethyl caffeate decreases the amount of VCPIP1. 1 / 1
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Nocodazole affects VCPIP1
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The samples were analyzed by SDS-PAGE and western blotting.For deubiquitination of Syn5 by immunoprecipitated VCIP135, HeLa cells were treated with 100 ng/ml nocodazole (Sigma) for 18 hr, washed five [MISSING/INVALID CREDENTIALS: limited to 200 char for Elsevier]
Miconazole affects VCPIP1
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Miconazole decreases the amount of VCPIP1. 1 / 1
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Ketamine affects VCPIP1
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Ketamine decreases the amount of VCPIP1. 1 / 1
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Jinfukang affects VCPIP1
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Jinfukang decreases the amount of VCPIP1. 1 / 1
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Ionomycin affects VCPIP1
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Ionomycin decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-943 decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-92a-3p decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-877-3p decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-7977 decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-675-5p decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-583 decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-5002-3p decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-4801 decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-4746-3p decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-4731-3p decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-4639-5p decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-4466 decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-4439 decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-4311 decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-4284 decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-383-3p decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-361-5p decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-3136-5p decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-24-3p decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-193b-3p decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-1827 decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-155-5p decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-1276 decreases the amount of VCPIP1. 1 / 1
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Hsa-miR-1260b decreases the amount of VCPIP1. 1 / 1
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Hexabromocyclododecane decreases the amount of VCPIP1. 1 / 1
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Glycitin affects VCPIP1
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Glycitin increases the amount of VCPIP1. 1 / 1
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Glycitein affects VCPIP1
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Glycitein increases the amount of VCPIP1. 1 / 1
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Genistein affects VCPIP1
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Genistein increases the amount of VCPIP1. 1 / 1
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Formaldehyde decreases the amount of VCPIP1. 1 / 1
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Fenofibrate increases the amount of VCPIP1. 1 / 1
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Diarsenic trioxide increases the amount of VCPIP1. 1 / 1
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Daidzein affects VCPIP1
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Daidzein increases the amount of VCPIP1. 1 / 1
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Copper(II) sulfate increases the amount of VCPIP1. 1 / 1
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Cobalt dichloride increases the amount of VCPIP1. 1 / 1
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Clorgyline affects VCPIP1
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Clorgyline increases the amount of VCPIP1. 1 / 1
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Cisplatin affects VCPIP1
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Cisplatin decreases the amount of VCPIP1. 1 / 1
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Butanal affects VCPIP1
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Butanal decreases the amount of VCPIP1. 1 / 1
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Bis(2-ethylhexyl) phthalate decreases the amount of VCPIP1. 1 / 1
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Benzo[a]pyrene increases the amount of VCPIP1. 1 / 1
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Beclomethasone decreases the amount of VCPIP1. 1 / 1
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Aflatoxin B1 increases the amount of VCPIP1. 1 / 1
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ZIC2 affects VCPIP1
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ZIC2 decreases the amount of VCPIP1. 1 / 1
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VCPIP1 affects elaD
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VCPIP1 inhibits elaD. 1 / 1
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Mitotic phosphorylation of VCIP135 at S130 inhibits its deubiquitinase activity.
VCPIP1 affects alphaSnap
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As shown in XREF_FIG G, VCIP135 partially prevented alpha-SNAP binding to GST-syn5DeltaTM, suggesting that VCIP135 directs syntaxin5 to p97 and p47 but not to alpha-SNAP and NSF.
U0126 affects VCPIP1
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U0126 activates VCPIP1. 1 / 1
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Dephosphorylation of S130 on VCIP135 upon staurosporine or roscovitine but not U0126 treatment also significantly increased the DUB activity of endogenous VCIP135 (XREF_FIG), consistent with the hypothesis that phosphorylation at S130 inactivates VCIP135.
T-2 Toxin affects VCPIP1
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T-2 Toxin decreases the amount of VCPIP1. 1 / 1
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Plant Oils affects VCPIP1
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Plant Oils increases the amount of VCPIP1. 1 / 1
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PAX5 affects VCPIP1
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PAX5 decreases the amount of VCPIP1. 1 / 1
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NSFL1C affects VCPIP1
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NSFL1C activates VCPIP1. 1 / 1
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WAC is hence thought to function in p97 and p47 mediated Golgi membrane fusion by activating the deubiquitinating function of VCIP135.
NRF1 affects VCPIP1
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NRF1 decreases the amount of VCPIP1. 1 / 1
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N-nitrosodiethylamine decreases the amount of VCPIP1. 1 / 1
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MYB affects VCPIP1
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MYB decreases the amount of VCPIP1. 1 / 1
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Infections affects VCPIP1
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Infections increases the amount of VCPIP1. 1 / 1
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In the present study, DTMUV infection induced differential expression of the deubiquitinating protein VCIP135, proteasome 26S subunit, and proteasome subunit beta.
HNF4A affects VCPIP1
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HNF4A decreases the amount of VCPIP1. 1 / 1
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FOXO4 affects VCPIP1
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FOXO4 decreases the amount of VCPIP1. 1 / 1
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ELK1 affects VCPIP1
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ELK1 decreases the amount of VCPIP1. 1 / 1
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Antirheumatic Agents decreases the amount of VCPIP1. 1 / 1
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AR affects VCPIP1
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AR decreases the amount of VCPIP1. 1 / 1
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17alpha-ethynylestradiol increases the amount of VCPIP1. 1 / 1
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