Abstract:
:The Library of Integrated Network-based Cellular Signatures (LINCS) L1000 big data provide gene expression profiles induced by over 10 000 compounds, shRNAs, and kinase inhibitors using the L1000 platform. We developed csNMF, a systematic compound signature discovery pipeline covering from raw L1000 data processing to drug screening and mechanism generation. The csNMF pipeline demonstrated better performance than the original L1000 pipeline. The discovered compound signatures of breast cancer were consistent with the LINCS KINOMEscan data and were clinically relevant. The csNMF pipeline provided a novel and complete tool to expedite signature-based drug discovery leveraging the LINCS L1000 resources.
journal_name
Mol Biosystjournal_title
Molecular bioSystemsauthors
Liu C,Su J,Yang F,Wei K,Ma J,Zhou Xdoi
10.1039/c4mb00677asubject
Has Abstractpub_date
2015-03-01 00:00:00pages
714-22issue
3eissn
1742-206Xissn
1742-2051journal_volume
11pub_type
杂志文章abstract::The adaptation of the cellular network to functional changes, timing and patterning of gene expression is regulated by binding of transcription factors to gene regulatory elements, which in turn depends on co-occurring histone modifications. These two layers influence each other, enabling a further level of regulatory...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c1mb05363a
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journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b801724g
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abstract::To understand the regulatory dynamics of transcription factors (TFs) and their interplay with other cellular components we have integrated transcriptional, protein-protein and the allosteric or equivalent interactions which mediate the physiological activity of TFs in Escherichia coli. To study this integrated network...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c2mb25279a
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journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00688g
更新日期:2015-04-01 00:00:00
abstract::The crystal structure of the versatile CYP109B1 enzyme from Bacillus subtilis has been solved at 1.8 Å resolution. This is the first structure of an enzyme from this CYP family, whose members are prevalent across diverse species of bacteria. In the crystal structure the enzyme has an open conformation with an access c...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00665h
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abstract::The transforming growth factor beta (TGF-β) signaling pathway plays myriad roles in development and disease. TGF-β isoforms initiate signaling by organizing their cell surface receptors TβRI and TβRII. Exploration and exploitation of the versatility of TGF-β signaling requires an enhanced understanding of structure-fu...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c0mb00115e
更新日期:2010-12-01 00:00:00
abstract::The search for molecules with activity against Mycobacterium tuberculosis (Mtb) is employing many approaches in parallel including high throughput screening and computational methods. We have developed a database (CDD TB) to capture public and private Mtb data while enabling data mining and collaborations with other r...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b917766c
更新日期:2010-05-01 00:00:00
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journal_title:Molecular bioSystems
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doi:10.1039/c5mb00273g
更新日期:2015-08-01 00:00:00
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journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00159e
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journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00217b
更新日期:2014-08-01 00:00:00
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journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b700547d
更新日期:2007-12-01 00:00:00
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journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c3mb70540d
更新日期:2014-04-01 00:00:00
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journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00214a
更新日期:2015-08-01 00:00:00
abstract::Protein tyrosine phosphatases are crucial regulators of signal transduction and function as antagonists towards protein tyrosine kinases to control reversible tyrosine phosphorylation, thereby regulating fundamental physiological processes. Growing evidence has supported the notion that reversible oxidative inactivati...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00847f
更新日期:2016-05-24 00:00:00
abstract::Endogenous thymidylate synthases, isolated from tissues or cultured cells of the same specific origin, have been reported to show differing slow-binding inhibition patterns. These were reflected by biphasic or linear dependence of the inactivation rate on time and accompanied by differing inhibition parameters. Consid...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c6mb00026f
更新日期:2016-04-01 00:00:00
abstract::Fabry disease (FD) is an X-linked lysosomal storage disorder caused by a deficiency of the lysosomal hydrolase α-galactosidase A (α-GalA) that leads to the intra-lysosomal accumulation of globotriaosylceramide (Gb3) in various organ systems. As a consequence, a multisystems disorder develops, culminating in stroke, pr...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00707g
更新日期:2015-06-01 00:00:00
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journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00308c
更新日期:2015-10-01 00:00:00
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journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00309a
更新日期:2015-09-01 00:00:00
abstract::Conversion of the predominantly α-helical cellular prion protein (PrP(C)) to the misfolded β-sheet enriched Scrapie form (PrP(Sc)) is a critical event in prion pathogenesis. However, the conformational triggers that lead to the isoform conversion (PrP(C) to PrP(Sc)) remain obscure, and conjectures about the role of un...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00689e
更新日期:2015-05-01 00:00:00
abstract::Unbalanced uptake of Omega 6/Omega 3 (ω-6/ω-3) ratios could increase chronic disease occurrences, such as inflammation, atherosclerosis, or tumor proliferation, and methylation methods for measuring the ruminal microbiome fatty acid (FA) composition/distribution play a vital role in discovering the contribution of foo...
journal_title:Molecular bioSystems
pub_type: 杂志文章
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journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b503302k
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journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00071h
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journal_title:Molecular bioSystems
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journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00413f
更新日期:2015-12-01 00:00:00
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journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c1mb05271c
更新日期:2011-11-01 00:00:00
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journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c6mb00154h
更新日期:2016-06-21 00:00:00
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journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00268k
更新日期:2015-09-01 00:00:00
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journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b908784b
更新日期:2010-01-01 00:00:00
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journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
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pub_type: 杂志文章,评审
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