SCAF11

Summary

Gene Symbol: SCAF11
Description: SR-related CTD associated factor 11
Alias: CASP11, SFRS2IP, SIP1, SRRP129, SRSF2IP, protein SCAF11, CTD-associated SR protein 11, SC35-interacting protein 1, SFRS2-interacting protein, SR-related and CTD-associated factor 11, SRSF2-interacting protein, renal carcinoma antigen NY-REN-40, serine/arginine-rich splicing factor 2-interacting protein, splicing factor, arginine/serine-rich 2-interacting protein, splicing regulatory protein 129
Species: human
Products:     SCAF11

Top Publications

  1. Zhang W, Wu J. Sip1, a novel RS domain-containing protein essential for pre-mRNA splicing. Mol Cell Biol. 1998;18:676-84 pubmed
    ..We report here identification and functional characterization of a new splicing factor, Sip1 (SC35-interacting protein 1)...
  2. Darr A, Danzi M, Brady L, Emig Agius D, Hackett A, Golshani R, et al. Identification of genome-wide targets of Olig2 in the adult mouse spinal cord using ChIP-Seq. PLoS ONE. 2017;12:e0186091 pubmed publisher
    ..2, Nkx6.2, and Sip1), myelination and ensheathment (Mbp, Cldn11, and Mobp), as well as cell cycle and cytoskeletal regulation...
  3. Serrano M, Liu J, Svoboda K, Nawshad A, Benson M. Ephrin reverse signaling mediates palatal fusion and epithelial-to-mesenchymal transition independently of Tgfß3. J Cell Physiol. 2015;230:2961-72 pubmed publisher
    ..They concurrently increased their expression of the EMT-associated transcription factors Snail, Sip1, and Twist1. EphB2/Fc did not cause apoptosis in these cells...
  4. Suzuki T, Sakumoto R, Hayashi K, Ogiso T, Kunii H, Shirozu T, et al. Involvement of interferon-tau in the induction of apoptotic, pyroptotic, and autophagic cell death-related signaling pathways in the bovine uterine endometrium during early pregnancy. J Reprod Dev. 2018;64:495-502 pubmed publisher
    ..in pregnant uterine tissue, IFNT affected the increase of apoptosis-related (CASP8) and pyroptosis-related genes (CASP11), but did not affect autophagy-related gene expression...
  5. Lutz G, Jurak I, Kim E, Kim J, Hackenberg M, Leader A, et al. Viral Ubiquitin Ligase Stimulates Selective Host MicroRNA Expression by Targeting ZEB Transcriptional Repressors. Viruses. 2017;9: pubmed publisher
    ..enhancer binding factor 1 (δEF1) and zinc finger E-box binding homeobox 2 (ZEB2)/Smad-interacting protein 1 (SIP1), which we establish as new substrates for ICP0-mediated degradation...
  6. Volk D, Edelson J, Lewis D. Altered expression of developmental regulators of parvalbumin and somatostatin neurons in the prefrontal cortex in schizophrenia. Schizophr Res. 2016;177:3-9 pubmed publisher
    ..Finally, expression levels of other important developmental regulators (i.e. Dlx1, Dlx5, Dlx6, SATB1, Sip1/Zeb2, ST8SIA4, cMaf, Nkx6.2, and Arx) were not altered in schizophrenia...
  7. León I, Díez P, Baran E, Etcheverry S, Fuentes M. Decoding the anticancer activity of VO-clioquinol compound: the mechanism of action and cell death pathways in human osteosarcoma cells. Metallomics. 2017;9:891-901 pubmed publisher
    ..differential protein expression levels reveal several up-regulated proteins such as CASP3, CASP6, CASP7, CASP10, CASP11, Bcl-x, DAPK and down-regulated ones, such as PKB/AKT, DIABLO, among others...
  8. Galindo Hernandez O, Serna Marquez N, Castillo Sanchez R, Salazar E. Extracellular vesicles from MDA-MB-231 breast cancer cells stimulated with linoleic acid promote an EMT-like process in MCF10A cells. Prostaglandins Leukot Essent Fatty Acids. 2014;91:299-310 pubmed publisher
    ..LA induce a transient down-regulation of E-cadherin expression, and an increase of Snail1 and 2, Twist1 and 2, Sip1, vimentin and N-cadherin expression in MCF10A cells...
  9. Qi X, Ng K, Lian Q, Liu X, Li C, Geng W, et al. Clinical significance and therapeutic value of glutathione peroxidase 3 (GPx3) in hepatocellular carcinoma. Oncotarget. 2014;5:11103-20 pubmed
    ..Tumor suppressive activity of GPx3 was mediated through Erk-NFκB-SIP1 pathway. GPx3 could be delivered by hiPSC-MSCs into the tumor and exhibited tumor suppressive activity in vivo...

More Information

Publications125 found, 100 shown here

  1. Alvarez Gerding X, Espinoza C, Inostroza Blancheteau C, Arce Johnson P. Molecular and physiological changes in response to salt stress in Citrus macrophylla W plants overexpressing Arabidopsis CBF3/DREB1A. Plant Physiol Biochem. 2015;92:71-80 pubmed publisher
    ..real-time analyses showed a similar expression of several CBF3/DREB1A target genes, such as COR15A, LEA 4/5, INV, SIP1, P5CS, GOLS, ADC2 and LKR/SDH, in transgenic lines and wild type plants, with the exception of INV that shows ..
  2. Okamoto Y, Nishimura N, Matsuda K, Ranawakage D, Kamachi Y, Kondoh H, et al. Cooperation of Sall4 and Sox8 transcription factors in the regulation of the chicken Sox3 gene during otic placode development. Dev Growth Differ. 2018;60:133-145 pubmed publisher
    ..The CAGGTG sequence likely serves as the binding sites of the repressor TFs ?EF1 (Zeb1), Sip1 (Zeb2), and Snail2, all of which are expressed in the cephalic neural crest but not in the otic placode...
  3. Basova L, Tang X, Umasume T, Gromova A, Zyrianova T, Shmushkovich T, et al. Manipulation of Panx1 Activity Increases the Engraftment of Transplanted Lacrimal Gland Epithelial Progenitor Cells. Invest Ophthalmol Vis Sci. 2017;58:5654-5665 pubmed publisher
    ..the LG of the TSP-1-/- mouse (mouse model of chronic LG inflammation) by either Panx1 or Caspase-4 (also known as Casp11) sdRNAi showed a significant decrease in expression of proinflammatory markers and the lymphocyte infiltration...
  4. Chen D, Liu G, Xu N, You X, Zhou H, Zhao X, et al. Knockdown of ARK5 Expression Suppresses Invasion and Metastasis of Gastric Cancer. Cell Physiol Biochem. 2017;42:1025-1036 pubmed publisher
    ..And knockdown of ARK5 expression in GC cells resulted in the down-regulation of the mTOR/p70S6k signals, Slug and SIP1. The elevated ARK5 expression was closely associated with cancer metastasis and patient survival, and it seemed to ..
  5. Schmidt R, Lenz L. Distinct licensing of IL-18 and IL-1β secretion in response to NLRP3 inflammasome activation. PLoS ONE. 2012;7:e45186 pubmed publisher
    ..Furthermore, DCs from caspase-11 (casp11)-deficient 129S6 mice failed to secrete IL-1β in response to p60 but were fully responsive for IL-18 secretion...
  6. Kok F, Shepherd I, Sirotkin H. Churchill and Sip1a repress fibroblast growth factor signaling during zebrafish somitogenesis. Dev Dyn. 2010;239:548-58 pubmed publisher
    ..ChCh is largely thought to act by inducing expression of the multifunctional Sip1 (Smad Interacting Protein 1). We investigated the function of ChCh and Sip1a during zebrafish somitogenesis...
  7. Błażejewski A, Thiemann S, Schenk A, Pils M, Gálvez E, Roy U, et al. Microbiota Normalization Reveals that Canonical Caspase-1 Activation Exacerbates Chemically Induced Intestinal Inflammation. Cell Rep. 2017;19:2319-2330 pubmed publisher
    ..To this end, we generated Casp1-/- and Casp11-/- mice and rederived them into an enhanced barrier facility to standardize the microbiota...
  8. Yu C, Cai X, Ye Z, Li H. Genome-wide identification and expression profiling analysis of trihelix gene family in tomato. Biochem Biophys Res Commun. 2015;468:653-9 pubmed publisher
    ..SlGT members can be classified into six subgroups (GT-1, GT-2, SH4, SIP1, GT-γ and GT-δ)...
  9. Kiliç E, Cetinkaya A, Utine G, BoduroÄŸlu K. A Diagnosis to Consider in Intellectual Disability: Mowat-Wilson Syndrome. J Child Neurol. 2016;31:913-7 pubmed publisher
    ..The condition is caused by de novo heterozygous mutations or deletions in ZEB2 gene located at 2q22. ZEB2 encodes Sip1 protein, which acts during central nervous system development as an important transcription factor...
  10. Zhao Y, Sun Y, Huang A, Li X, Huang C, Ma T, et al. MicroRNA-200a induces apoptosis by targeting ZEB2 in alcoholic liver disease. Cell Cycle. 2017;:1-32 pubmed publisher
    ..examined it's effect on cell apoptosis and identified zinc finger E-box binding homeobox 2 (ZEB2; also known as SIP1) as a direct target gene of miR-200a...
  11. Sanz P, Viana R, Garcia Gimeno M. AMPK in Yeast: The SNF1 (Sucrose Non-fermenting 1) Protein Kinase Complex. Exp Suppl. 2016;107:353-374 pubmed
    ..orthologue of AMPKα catalytic subunit), Snf4 (orthologue of AMPKγ regulatory subunit), and a member of the Gal83/Sip1/Sip2 family of proteins (orthologues of AMPKβ subunit) that act as scaffolds and also regulate the subcellular ..
  12. Yang D, He Y, Muñoz Planillo R, Liu Q, Núñez G. Caspase-11 Requires the Pannexin-1 Channel and the Purinergic P2X7 Pore to Mediate Pyroptosis and Endotoxic Shock. Immunity. 2015;43:923-32 pubmed publisher
    ..TLR3) agonist resulted in high mortality in wild-type mice after secondary LPS challenge, but not in Casp11(-/-), Panx1(-/-), or P2x7(-/-) mice...
  13. Adhikari B, Cheng J. CONFOLD2: improved contact-driven ab initio protein structure modeling. BMC Bioinformatics. 2018;19:22 pubmed publisher
    ..57 TM-score for the 150 proteins in the PSICOV contact prediction dataset. When benchmarked on the CASP11 contacts predicted using CONSIP2 and CASP12 contacts predicted using Raptor-X, CONFOLD2 achieves a mean TM-score ..
  14. Singh A, Kaushik R, Mishra A, Shanker A, Jayaram B. ProTSAV: A protein tertiary structure analysis and validation server. Biochim Biophys Acta. 2016;1864:11-9 pubmed publisher
    ..solved structures and achieves a specificity of 88%and a sensitivity of 91% on predicted protein structures of CASP11 targets under 2Ã…...
  15. Wang S, Li W, Liu S, Xu J. RaptorX-Property: a web server for protein structure property prediction. Nucleic Acids Res. 2016;44:W430-5 pubmed publisher
    ..Our experimental results show that, tested on CASP10, CASP11 and the other benchmarks, this server can obtain ∼84% Q3 accuracy for 3-state SS, ∼72% Q8 accuracy for 8-..
  16. Hoshi Y, Endo K, Shirakihara T, Fukagawa A, Miyazawa K, Saitoh M. The potential role of regulator of G-protein signaling 16 in cell motility mediated by δEF1 family proteins. FEBS Lett. 2016;590:270-8 pubmed publisher
    ..We reported previously that expression of the δEF1 family proteins (δEF1/ZEB1 and SIP1/ZEB2), key regulators of the EMT, is positively correlated with EMT phenotypes and aggressiveness of breast cancer...
  17. Deng L, Fan C, Zeng Z. A sparse autoencoder-based deep neural network for protein solvent accessibility and contact number prediction. BMC Bioinformatics. 2017;18:569 pubmed publisher
    ..We also evaluate the performance on the CASP11 benchmark dataset, DeepSacon achieves 0.68 three-state accuracy and 0...
  18. Zhang B, Li J, Lu Q. Prediction of 8-state protein secondary structures by a novel deep learning architecture. BMC Bioinformatics. 2018;19:293 pubmed publisher
    ..Our model generalization capability is also evaluated on other three independent datasets CASP10, CASP11 and CASP12 for both 8- and 3-state prediction...
  19. Mabrouk M, Putz I, Werner T, Schneider M, Neeb M, Bartels P, et al. RBO Aleph: leveraging novel information sources for protein structure prediction. Nucleic Acids Res. 2015;43:W343-8 pubmed publisher
    ..and contact prediction during the most recent Critical Assessment of Protein Structure Prediction experiment (CASP11, 2014)...
  20. Miyazawa S. Prediction of Structures and Interactions from Genome Information. Adv Exp Med Biol. 2018;1105:123-152 pubmed publisher
    ..However, contact prediction accuracies of methods evaluated in CASP experiments before CASP11 remained quite low, typically with <20% true positives...
  21. Han X, Li L, Lu Y. Selecting Near-Native Protein Structures from Predicted Decoy Sets Using Ordered Graphlet Degree Similarity. Genes (Basel). 2019;10: pubmed publisher
    ..The proposed method was applied to all 54 single-domain targets in CASP11 and all 43 targets in CASP10, and ensemble clustering was used to cluster the protein decoy structures based on ..
  22. Jing X, Dong Q. MQAPRank: improved global protein model quality assessment by learning-to-rank. BMC Bioinformatics. 2017;18:275 pubmed publisher
    ..Benchmarked on CASP11 and 3DRobot datasets, the MQAPRank achieved better performances than other leading protein model quality ..
  23. Rawi R, Mall R, Kunji K, El Anbari M, Aupetit M, Ullah E, et al. COUSCOus: improved protein contact prediction using an empirical Bayes covariance estimator. BMC Bioinformatics. 2016;17:533 pubmed
    ..achieves on average 10% more gain in prediction accuracy compared to PSICOV on an independent test set composed of CASP11 protein targets...
  24. Ma Y, Liu Y, Cheng J. Protein Secondary Structure Prediction Based on Data Partition and Semi-Random Subspace Method. Sci Rep. 2018;8:9856 pubmed publisher
    ..Experiments are performed on 25PDB, CB513, CASP10, CASP11, CASP12, and T100 datasets, and the good performance of 86.38%, 84.53%, 85.51%, 85.89%, 85.55%, and 85...
  25. Cao R, Bhattacharya D, Hou J, Cheng J. DeepQA: improving the estimation of single protein model quality with deep belief networks. BMC Bioinformatics. 2016;17:495 pubmed
    ..the protein model quality assessment problem, and our method DeepQA achieves the state-of-the-art performance on CASP11 dataset...
  26. Heo L, Feig M. PREFMD: a web server for protein structure refinement via molecular dynamics simulations. Bioinformatics. 2017;: pubmed publisher
    ..The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in global ..
  27. He Y, Rackovsky S, Yin Y, Scheraga H. Alternative approach to protein structure prediction based on sequential similarity of physical properties. Proc Natl Acad Sci U S A. 2015;112:5029-32 pubmed publisher
    ..than that of PSI BLAST when sequence matching is comparable, based on a comparison using targets from CASP10 (89 targets) and CASP11 (51 targets). It is also shown that PFM outperforms PSI BLAST in informatically challenging targets.
  28. Xu H, Shi X, He L, Guo Y, Zang D, Li H, et al. Arabidopsis thaliana Trihelix Transcription Factor AST1 Mediates Salt and Osmotic Stress Tolerance by Binding to a Novel AGAG-Box and Some GT Motifs. Plant Cell Physiol. 2018;59:946-965 pubmed publisher
    ..In the present study, we characterized the function of AST1 (Arabidopsis SIP1 clade Trihelix1) in response to salt and osmotic stress...
  29. Flood B, Manils J, Nulty C, Flis E, Kenealy S, Barber G, et al. Caspase-11 regulates the tumour suppressor function of STAT1 in a murine model of colitis-associated carcinogenesis. Oncogene. 2019;38:2658-2674 pubmed publisher
    ..Here, we show that Casp11-/- mice are highly susceptible to the azoxymethane (AOM)-DSS model of colitis-associated cancer (CAC), ..
  30. Mabrouk M, Werner T, Schneider M, Putz I, Brock O. Analysis of free modeling predictions by RBO aleph in CASP11. Proteins. 2016;84 Suppl 1:87-104 pubmed publisher
    The CASP experiment is a biannual benchmark for assessing protein structure prediction methods. In CASP11, RBO Aleph ranked as one of the top-performing automated servers in the free modeling category...
  31. Chen D, You X, Pan Y, Liu Q, Cao G. TRIM37 promotes cell invasion and metastasis by regulating SIP1-mediated epithelial-mesenchymal transition in gastric cancer. Onco Targets Ther. 2018;11:8803-8813 pubmed publisher
    ..Inversely, TRIM37 overexpression exerted the opposite effects. Mechanistic studies suggested that SIP1-mediated EMT might be responsible for TRIM37-facilitated GC cells migration and invasion...
  32. West T, Myers N, Chantratita N, Chierakul W, Limmathurotsakul D, Wuthiekanun V, et al. NLRC4 and TLR5 each contribute to host defense in respiratory melioidosis. PLoS Negl Trop Dis. 2014;8:e3178 pubmed publisher
    ..Mice deficient in both Tlr5 and Nlrc4 were not more susceptible than single knockout animals. Deficiency of Casp1/Casp11 resulted in impaired bacterial control in the lung and spleen; in the lung much of this effect was attributable to ..
  33. Wang Z, Zhao K, Pan Y, Wang J, Song X, Ge W, et al. Genomic, expressional, protein-protein interactional analysis of Trihelix transcription factor genes in Setaria italia and inference of their evolutionary trajectory. BMC Genomics. 2018;19:665 pubmed publisher
    ..Six amino acid sites of the SIP1 subfamily possibly were likely subjected to significant positive selection...
  34. Wu L, Wang J, Conidi A, Zhao C, Wang H, Ford Z, et al. Zeb2 recruits HDAC-NuRD to inhibit Notch and controls Schwann cell differentiation and remyelination. Nat Neurosci. 2016;19:1060-72 pubmed publisher
    ..Here we demonstrate that zinc-finger E-box-binding homeobox 2 (Zeb2, also called Sip1) transcription factor is a critical intrinsic timer that controls the onset of SC differentiation by recruiting ..
  35. Keasar C, McGuffin L, Wallner B, Chopra G, Adhikari B, Bhattacharya D, et al. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Sci Rep. 2018;8:9939 pubmed publisher
    ..Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research. ..
  36. Zhou Z, Sun B, Sun L. Edwardsiella tarda Sip1: A serum-induced zinc metalloprotease that is essential to serum resistance and host infection. Vet Microbiol. 2015;177:332-40 pubmed publisher
    ..Five differentially expressed proteins were identified, one of which was a putative zinc protease (named Sip1). Western blot confirmed extracellular production of Sip1 by E. tarda...
  37. Della Corte D, Wildberg A, Schröder G. Protein structure refinement with adaptively restrained homologous replicas. Proteins. 2016;84 Suppl 1:302-13 pubmed publisher
    ..It is shown that this protocol refines the majority of models from the CASP11 refinement category and that larger conformational changes of the starting structure are possible than with ..
  38. Ovchinnikov S, Kim D, Wang R, Liu Y, DiMaio F, Baker D. Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta. Proteins. 2016;84 Suppl 1:67-75 pubmed publisher
    We describe CASP11 de novo blind structure predictions made using the Rosetta structure prediction methodology with both automatic and human assisted protocols...
  39. Turovskaya M, Zinchenko V, Babaev A, Epifanova E, Tarabykin V, Turovsky E. Mutation in the Sip1 transcription factor leads to a disturbance of the preconditioning of AMPA receptors by episodes of hypoxia in neurons of the cerebral cortex due to changes in their activity and subunit composition. The protective effects of int. Arch Biochem Biophys. 2018;654:126-135 pubmed publisher
    The Sip1 mutation plays the main role in pathogenesis of the Mowat-Wilson syndrome, which is characterized by the pronounced epileptic symptoms...
  40. Barbu E, Zhang J, Berenstein E, Groves J, Parks L, Siraganian R. The transcription factor Zeb2 regulates signaling in mast cells. J Immunol. 2012;188:6278-86 pubmed publisher
    ..We found that Zeb2 (also named Sip1, Zfhx1b), a zinc finger transcription factor, regulates both early and late mast cell responses...
  41. Abeysundara N, Leung A, Primrose D, Hughes S. Regulation of cell proliferation and adhesion by means of a novel region of drosophila merlin interacting with Sip1. Dev Dyn. 2014;243:1554-70 pubmed publisher
    ..We investigate how the Drosophila NHERF1 orthologue, Sip1, and Merlin function to regulate cell proliferation and adhesion...
  42. Williams T, Leeth R, Rothschild D, McDaniel D, Coutermarsh Ott S, Simmons A, et al. Caspase-11 attenuates gastrointestinal inflammation and experimental colitis pathogenesis. Am J Physiol Gastrointest Liver Physiol. 2015;308:G139-50 pubmed publisher
    ..noncanonical inflammasome during inflammatory bowel disease, experimental colitis was induced in wild-type and Casp11(-/-) mice utilizing dextran sulfate sodium (DSS)...
  43. Bergsbaken T, Bevan M. Cutting Edge: Caspase-11 Limits the Response of CD8+ T Cells to Low-Abundance and Low-Affinity Antigens. J Immunol. 2015;195:41-5 pubmed publisher
    ..We report that caspase-11-deficient (Casp11(-/-)) T cells proliferated more readily in response to low-affinity and low-abundance ligands both in vitro and in ..
  44. Sun X, Sun Z, Zhu Z, Li C, Zhang J, Xu H, et al. Expression of SIP1 is strongly correlated with LDHA and shows a significantly poor outcome in gastric cancer. Tumour Biol. 2015;36:7521-30 pubmed publisher
    Smad interacting protein 1 (SIP1) plays an important role in the epithelial-mesenchymal transition (EMT) process by downregulating E-cadherin...
  45. Kim H, Kihara D. Protein structure prediction using residue- and fragment-environment potentials in CASP11. Proteins. 2016;84 Suppl 1:105-17 pubmed publisher
    ..Proteins 2016; 84(Suppl 1):105-117. © 2015 Wiley Periodicals, Inc. ..
  46. Xu G, Zhang L, Ma A, Qian Y, Ding Q, Liu Y, et al. SIP1 is a downstream effector of GADD45G in senescence induction and growth inhibition of liver tumor cells. Oncotarget. 2015;6:33636-47 pubmed publisher
    ..Here, we report that the Smad-interacting protein-1 (SIP1) is transcriptionally activated and functions critically in the GADD45G-induced tumor cell senescence...
  47. Jouppila Mättö A, Mannermaa A, Sironen R, Kosma V, Soini Y, Pukkila M. SIP1 predicts progression and poor prognosis in pharyngeal squamous cell carcinoma. Histol Histopathol. 2015;30:569-79 pubmed publisher
    ..The transcription factors SIP1, SLUG, ZEB1, SNAI1, and TWIST are fundamental in regulating EMT...
  48. Kinch L, Li W, Monastyrskyy B, Kryshtafovych A, Grishin N. Assessment of CASP11 contact-assisted predictions. Proteins. 2016;84 Suppl 1:164-80 pubmed publisher
    ..of contact-assisted predictions in the eleventh round of critical assessment of protein structure prediction (CASP11), which included four categories: predicted contacts (Tp), correct contacts (Tc), simulated sparse NMR contacts (..
  49. Fukagawa A, Ishii H, Miyazawa K, Saitoh M. δEF1 associates with DNMT1 and maintains DNA methylation of the E-cadherin promoter in breast cancer cells. Cancer Med. 2015;4:125-35 pubmed publisher
    ..EF1 family proteins (δEF1/ZEB1 and SIP1/ZEB2), key regulators of the epithelial-mesenchymal transition (EMT), suppress E-cadherin expression at the ..
  50. Srivatsa S, Parthasarathy S, Molnár Z, Tarabykin V. Sip1 downstream Effector ninein controls neocortical axonal growth, ipsilateral branching, and microtubule growth and stability. Neuron. 2015;85:998-1012 pubmed publisher
    b>Sip1 is an important transcription factor that regulates several aspects of CNS development...
  51. Xiao L, Zhou X, Liu F, Hu C, Zhu X, Luo Y, et al. MicroRNA-129-5p modulates epithelial-to-mesenchymal transition by targeting SIP1 and SOX4 during peritoneal dialysis. Lab Invest. 2015;95:817-832 pubmed publisher
    ..cell line (HPMC), treated with TGF-β1, whereas expression of vimentin, fibronectin and transcription factors SIP1 and SOX4 increased significantly, as assessed by real-time PCR, western blot analysis and immunofluorescence ..
  52. Yang L, Wang Y, Shi Y, Bu H, Ye F. Deletion of SIP1 promotes liver regeneration and lipid accumulation. Pathol Res Pract. 2016;212:421-5 pubmed publisher
    The function of Smad interacting protein-1 (SIP1) in liver regeneration is not yet known...
  53. Liu Y, Siles L, Lu X, Dean K, Cuatrecasas M, Postigo A, et al. Mitotic polarization of transcription factors during asymmetric division establishes fate of forming cancer cells. Nat Commun. 2018;9:2424 pubmed publisher
    ..In these cells, Zeb1 represses the Smad inhibitor Zeb2/Sip1, causing Pten loss and launching Tgf-β1 signaling that drives nuclear translocation of Yap1...
  54. Yang J, Zhang W, He B, Walker S, Zhang H, Govindarajoo B, et al. Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade. Proteins. 2016;84 Suppl 1:233-46 pubmed publisher
    ..Proteins 2016; 84(Suppl 1):233-246. © 2015 Wiley Periodicals, Inc. ..
  55. Wang C, Chen Q, Xiang N, Liu Y, Kong X, Yang Y, et al. SIP1, a novel SOS2 interaction protein, is involved in salt-stress tolerance in Arabidopsis. Plant Physiol Biochem. 2018;124:167-174 pubmed publisher
    ..protein was identified by yeast two hybrid (Y2H) library and was referred to as SOS2 interaction protein 1 (SIP1)...
  56. Bhardwaj M, Sen S, Sharma A, Kashyap S, Chosdol K, Pushker N, et al. ZEB2/SIP1 as novel prognostic indicator in eyelid sebaceous gland carcinoma. Hum Pathol. 2015;46:1437-42 pubmed publisher
    ..ZEB2/SIP1 is an important EMT regulator and down-regulates E-cadherin expression...
  57. Joo K, Joung I, Cheng Q, Lee S, Lee J. Contact-assisted protein structure modeling by global optimization in CASP11. Proteins. 2016;84 Suppl 1:189-99 pubmed publisher
    We have applied the conformational space annealing method to the contact-assisted protein structure modeling in CASP11. For Tp targets, where predicted residue-residue contact information was provided, the contact energy term in the form ..
  58. Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. Critical assessment of methods of protein structure prediction: Progress and new directions in round XI. Proteins. 2016;84 Suppl 1:4-14 pubmed publisher
    ..Here we report new developments and progress from the CASP11 community experiment, assessing the state of the art in structure modeling...
  59. Lee B, Stowe I, Gupta A, Kornfeld O, Roose Girma M, Anderson K, et al. Caspase-11 auto-proteolysis is crucial for noncanonical inflammasome activation. J Exp Med. 2018;215:2279-2288 pubmed publisher
    ..Macrophages from caspase-11-processing dead KI mice (Casp11Prc D285A/D285A ) exhibit defective caspase-11 auto-processing and phenocopy Casp11-/-<..
  60. Li A, Omura N, Hong S, Vincent A, Walter K, Griffith M, et al. Pancreatic cancers epigenetically silence SIP1 and hypomethylate and overexpress miR-200a/200b in association with elevated circulating miR-200a and miR-200b levels. Cancer Res. 2010;70:5226-37 pubmed publisher
    ..We also identified prevalent hypermethylation and silencing of one of their downstream targets, SIP1 (ZFHX1B, ZEB2), whose protein product suppresses E-cadherin expression and contributes to epithelial mesenchymal ..
  61. Aslanidis A, Karlstetter M, Scholz R, Fauser S, Neumann H, Fried C, et al. Activated microglia/macrophage whey acidic protein (AMWAP) inhibits NFκB signaling and induces a neuroprotective phenotype in microglia. J Neuroinflammation. 2015;12:77 pubmed publisher
    ..lipopolysaccharide (LPS)-activated microglia and recombinant AMWAP reduced gene transcription of IL6, iNOS, CCL2, CASP11, and TNFα in BV-2 microglia treated with LPS as TLR4 ligand...
  62. Li J, Adhikari B, Cheng J. An Improved Integration of Template-Based and Template-Free Protein Structure Modeling Methods and its Assessment in CASP11. Protein Pept Lett. 2015;22:586-93 pubmed
    ..participated in the 11(th) community-wide Critical Assessment of Techniques for Protein Structure Prediction (CASP11) in 2014 as MULTICOM-NOVEL server...
  63. Kryshtafovych A, Barbato A, Monastyrskyy B, Fidelis K, Schwede T, Tramontano A. Methods of model accuracy estimation can help selecting the best models from decoy sets: Assessment of model accuracy estimations in CASP11. Proteins. 2016;84 Suppl 1:349-69 pubmed publisher
    The article presents assessment of the model accuracy estimation methods participating in CASP11. The results of the assessment are expected to be useful to both-developers of the methods and users who way too often are presented with ..
  64. Kinch L, Li W, Monastyrskyy B, Kryshtafovych A, Grishin N. Evaluation of free modeling targets in CASP11 and ROLL. Proteins. 2016;84 Suppl 1:51-66 pubmed publisher
    ..The CASP11 FM category included several outstanding examples, including successful prediction by the Baker group of a 256-..
  65. Modi V, Dunbrack R. Assessment of refinement of template-based models in CASP11. Proteins. 2016;84 Suppl 1:260-81 pubmed publisher
    b>CASP11 (the 11th Meeting on the Critical Assessment of Protein Structure Prediction) ran a blind experiment in the refinement of protein structure predictions, the fourth such experiment since CASP8...
  66. Kimura Y, Irie K, Mizuno T. Expression control of the AMPK regulatory subunit and its functional significance in yeast ER stress response. Sci Rep. 2017;7:46713 pubmed publisher
    ..However, it remains unclear how the alternate three ? subunits, Sip1, Sip2, and Gal83, of the Snf1 complex participate in ER stress response...
  67. Turovskaya M, Babaev A, Zinchenko V, Epifanova E, Borisova E, Tarabykin V, et al. Sip-1 mutations cause disturbances in the activity of NMDA- and AMPA-, but not kainate receptors of neurons in the cerebral cortex. Neurosci Lett. 2017;650:180-186 pubmed publisher
    Smad-interacting protein-1 (Sip1) [Zinc finger homeobox (Zfhx1b), Zeb2] is a transcription factor implicated in the genesis of Mowat-Wilson syndrome (MWS) in humans...
  68. Stahl K, Schneider M, Brock O. EPSILON-CP: using deep learning to combine information from multiple sources for protein contact prediction. BMC Bioinformatics. 2017;18:303 pubmed publisher
    ..The different information sources are combined using deep neural networks. On 21 hard CASP11 FM targets, EPSILON-CP achieves a mean precision of 35...
  69. Zhang W, Yang J, He B, Walker S, Zhang H, Govindarajoo B, et al. Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11. Proteins. 2016;84 Suppl 1:76-86 pubmed publisher
    We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment...
  70. Wu Y, Chung I, Wong W, Masamune A, Sim M, Looi C. Paracrine IL-6 signaling mediates the effects of pancreatic stellate cells on epithelial-mesenchymal transition via Stat3/Nrf2 pathway in pancreatic cancer cells. Biochim Biophys Acta Gen Subj. 2017;1861:296-306 pubmed publisher
    ..and invasion capacity, and mesenchymal-like gene expression of N-cadherin, vimentin, fibronectin, collagen I, Sip1, Snail, Slug, and Twist2. Inhibition of JAK/Stat3 signaling induced by IL-6 repressed EMT and Nrf2 gene expression...
  71. Feig M, Mirjalili V. Protein structure refinement via molecular-dynamics simulations: What works and what does not?. Proteins. 2016;84 Suppl 1:282-92 pubmed publisher
    Protein structure refinement during CASP11 by the Feig group was described. Molecular dynamics simulations were used in combination with an improved selection and averaging protocol...
  72. Kryshtafovych A, Moult J, Baslé A, Burgin A, Craig T, Edwards R, et al. Some of the most interesting CASP11 targets through the eyes of their authors. Proteins. 2016;84 Suppl 1:34-50 pubmed publisher
    ..In this article, selected crystallographers providing targets for the CASP11 experiment discuss the functional and biological significance of the target proteins, highlight their most ..
  73. Schneider M, Belsom A, Rappsilber J, Brock O. Blind testing of cross-linking/mass spectrometry hybrid methods in CASP11. Proteins. 2016;84 Suppl 1:152-63 pubmed publisher
    ..CLMS data based on this protocol, submitted the data to the CASP organizers which then released this data to the CASP11 prediction groups in a separate, CLMS assisted modeling experiment...
  74. Li J, Cao R, Cheng J. A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11. BMC Bioinformatics. 2015;16:337 pubmed publisher
    ..MULTICOM-CLUSTER that participated in the 11th Critical Assessment of Techniques for Protein Structure Prediction (CASP11) in 2014. The two servers were ranked among the best 10 server predictors...
  75. Pires B, Mencalha A, Ferreira G, de Souza W, Morgado Diaz J, Maia A, et al. NF-kappaB Is Involved in the Regulation of EMT Genes in Breast Cancer Cells. PLoS ONE. 2017;12:e0169622 pubmed publisher
    ..related to the expression of the epithelial-to-mesenchymal transition transcription factors (EMT-TFs) SNAIL, SLUG, SIP1 and TWIST1...
  76. Ovchinnikov S, Park H, Kim D, Liu Y, Wang R, Baker D. Structure prediction using sparse simulated NOE restraints with Rosetta in CASP11. Proteins. 2016;84 Suppl 1:181-8 pubmed publisher
    In CASP11 we generated protein structure models using simulated ambiguous and unambiguous nuclear Overhauser effect (NOE) restraints with a two stage protocol...
  77. Lensink M, Velankar S, Kryshtafovych A, Huang S, Schneidman Duhovny D, Sali A, et al. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins. 2016;84 Suppl 1:323-48 pubmed publisher
    ..The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014...
  78. Park H, DiMaio F, Baker D. CASP11 refinement experiments with ROSETTA. Proteins. 2016;84 Suppl 1:314-22 pubmed publisher
    ..tackling the major issues that confound protein structure refinement, and the testing of these approaches in the CASP11 experiment...
  79. Joo K, Joung I, Lee S, Kim J, Cheng Q, Manavalan B, et al. Template based protein structure modeling by global optimization in CASP11. Proteins. 2016;84 Suppl 1:221-32 pubmed publisher
    For the template-based modeling (TBM) of CASP11 targets, we have developed three new protein modeling protocols (nns for server prediction and LEE and LEER for human prediction) by improving upon our previous CASP protocols (CASP7 through ..
  80. Kosciolek T, Jones D. Accurate contact predictions using covariation techniques and machine learning. Proteins. 2016;84 Suppl 1:145-51 pubmed publisher
    Here we present the results of residue-residue contact predictions achieved in CASP11 by the CONSIP2 server, which is based around our MetaPSICOV contact prediction method...
  81. Cao R, Bhattacharya D, Adhikari B, Li J, Cheng J. Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11. Proteins. 2016;84 Suppl 1:247-59 pubmed publisher
    ..that was successfully benchmarked in the 11th Critical Assessment of Techniques of Protein Structure prediction (CASP11)...
  82. Yasumi T, Inoue M, Maruhashi M, Kamachi Y, Higashi Y, Kondoh H, et al. Regulation of trunk neural crest delamination by δEF1 and Sip1 in the chicken embryo. Dev Growth Differ. 2016;58:205-14 pubmed publisher
    The vertebrate Zfhx1 transcription factor family comprises δEF1 and Sip1, which bind to CACCT-containing sequences and act as transcriptional repressors...
  83. Monastyrskyy B, D Andrea D, Fidelis K, Tramontano A, Kryshtafovych A. New encouraging developments in contact prediction: Assessment of the CASP11 results. Proteins. 2016;84 Suppl 1:131-44 pubmed publisher
    ..intra-molecular residue-residue contacts in proteins based on the assessment of the predictions submitted to the CASP11 experiment. The assessment emphasis is placed on the accuracy in predicting long-range contacts...
  84. Joung I, Lee S, Cheng Q, Kim J, Joo K, Lee S, et al. Template-free modeling by LEE and LEER in CASP11. Proteins. 2016;84 Suppl 1:118-30 pubmed publisher
    For the template-free modeling of human targets of CASP11, we utilized two of our modeling protocols, LEE and LEER...
  85. Quintes S, Brinkmann B, Ebert M, Fröb F, Kungl T, Arlt F, et al. Zeb2 is essential for Schwann cell differentiation, myelination and nerve repair. Nat Neurosci. 2016;19:1050-1059 pubmed publisher
    ..Here we show that transcriptional repression, mediated by the zinc-finger protein Zeb2 (also known as Sip1), is essential for differentiation and myelination...
  86. Takagi T, Nishizaki Y, Matsui F, Wakamatsu N, Higashi Y. De novo inbred heterozygous Zeb2/Sip1 mutant mice uniquely generated by germ-line conditional knockout exhibit craniofacial, callosal and behavioral defects associated with Mowat-Wilson syndrome. Hum Mol Genet. 2015;24:6390-402 pubmed publisher
    Mowat-Wilson syndrome (MOWS) is caused by de novo heterozygous mutation at ZEB2 (SIP1, ZFHX1B) gene, and exhibit moderate to severe intellectual disability (ID), a characteristic facial appearance, epilepsy and other congenital anomalies...
  87. Kinch L, Li W, Schaeffer R, Dunbrack R, Monastyrskyy B, Kryshtafovych A, et al. CASP 11 target classification. Proteins. 2016;84 Suppl 1:20-33 pubmed publisher
    Protein target structures for the Critical Assessment of Structure Prediction round 11 (CASP11) and CASP ROLL were split into domains and classified into categories suitable for assessment of template-based modeling (TBM) and free ..
  88. Kryshtafovych A, Monastyrskyy B, Fidelis K. CASP11 statistics and the prediction center evaluation system. Proteins. 2016;84 Suppl 1:15-9 pubmed publisher
    We outline the role of the Protein Structure Prediction Center (predictioncenter.org) in conducting the CASP11 and CASP ROLL experiments, discuss the experiment statistics, and provide an overview of the present CASP infrastructure...
  89. Sathyanarayanan A, Chandrasekaran K, Karunagaran D. microRNA-145 modulates epithelial-mesenchymal transition and suppresses proliferation, migration and invasion by targeting SIP1 in human cervical cancer cells. Cell Oncol (Dordr). 2017;40:119-131 pubmed publisher
    ..The identification of the SMAD-interacting protein 1 (SIP1) mRNA as putative miR-145 target was investigated using a 3' untranslated region (3'UTR) luciferase assay and ..
  90. Zhao W, Zhang S, Huang W, Li X. Mutations in Smad-interacting protein 1 gene are responsible for absence of its expression in Hirschsprung's disease. Clin Exp Med. 2018;18:445-451 pubmed publisher
    ..The pathophysiological basis remains unclear. Recently, the SIP1 gene has been recognized as being involved in the pathogenesis of symptomatic HSCR patients with 2q22 chromosomal ..
  91. Zhang H, Gao Y, Deng M, Wang C, Zhu J, Li S, et al. Improving residue-residue contact prediction via low-rank and sparse decomposition of residue correlation matrix. Biochem Biophys Res Commun. 2016;472:217-22 pubmed publisher
    ..We trained our LRS-based method on the PSICOV dataset, and tested it on both GREMLIN and CASP11 datasets. Our experimental results suggested that LRS significantly improves the contact prediction precision...
  92. Modi V, Xu Q, Adhikari S, Dunbrack R. Assessment of template-based modeling of protein structure in CASP11. Proteins. 2016;84 Suppl 1:200-20 pubmed publisher
    We present the assessment of predictions submitted in the template-based modeling (TBM) category of CASP11 (Critical Assessment of Protein Structure Prediction)...