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coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers

Alena van Bömmel, Michael I. Love, Ho-Ryun Chung, Martin Vingron, Patrick Cahan
2018 PLoS Computational Biology  
OPEN ACCESS Citation: van Bömmel A, Love MI, Chung H-R, Vingron M (2018) coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers. PLoS Comput Biol 14(8): e1006372.  ...  In summary, coTRaCTE predicts highly cell-type specific co-occurring TFs which reveal new insights into transcriptional regulatory mechanisms.  ...  Co-occurrence of TFs within cell-type specific enhancers To predict pairs of co-occuring TFs in a cell-type specific manner, we quantify (i) the degree of overlap between cell-type specific DHSs (corresponding  ... 
doi:10.1371/journal.pcbi.1006372 pmid:30142147 fatcat:ud5hcz4vdvhhhogpup3vrkn4mm

TF-COMB - discovering grammar of transcription factor binding sites [article]

Mette Bentsen, Vanessa Heger, Hendrik Schultheis, Carsten Kuenne, Mario Looso
2022 bioRxiv   pre-print
Here we present TF-COMB (Transcription Factor Co-Occurrence using Market Basket analysis) - a tool to investigate co-occurring TFs and binding grammar within regulatory regions.  ...  Cooperativity between transcription factors is important to regulate target gene expression.  ...  Here we introduce the TF-COMB (Transcription Factor Co-Occurrence using Market Basket analysis) framework, which uses an enhanced market basket analysis to identify and investigate the grammar of co-occurring  ... 
doi:10.1101/2022.06.21.496953 fatcat:5dzkvci6wbfejczm6buzvciwke

MEDEA: analysis of transcription factor binding motifs in accessible chromatin

Luca Mariani, Kathryn Weinand, Stephen S. Gisselbrecht, Martha L. Bulyk
2020 Genome Research  
Here, we present motif enrichment in differential elements of accessibility (MEDEA), a computational tool that analyzes high-throughput chromatin accessibility genomic data to identify cell-type-specific  ...  Deciphering the interplay between chromatin accessibility and transcription factor (TF) binding is fundamental to understanding transcriptional regulation, control of cellular states, and the establishment  ...  We thank Alena van Bömmel and Martin Vingron (Max Planck Institute) for help with coTRaCTE. We thank the members of the Bulyk laboratory for discussions and suggestions.  ... 
doi:10.1101/gr.260877.120 pmid:32424069 pmcid:PMC7263192 fatcat:svaaov6w45cslfymlqblacijum

Thirty-seventh Annual Meeting February 14-18, 1993 Washington Convention Center Washington, D.C. Wednesday Symposia and Posters, Part III

1993 Biophysical Journal  
This clearance depends upon both the mucus secreted by the goblet cells and the microtubule-based ciliary beat frequency (CBF) of airway epithelial cells.  ...  To determine changes in CBF and [Ca2+]i of the same cell, tracheal epithelial cells were obtained from sheep by dissociation with protease and grown in culture for 2-14 days.  ...  The major factor in cotraction as in thermodynamic stability is the arrangement of peptide dipokls Comparisons of B-factor plots for different kinds of atoms can give rare information about these arrayL  ... 
doi:10.1016/s0006-3495(93)81410-3 fatcat:wwy72envojaprjz5fgeuktvxte

Thirty-Fourth Annual Meeting February 18–22, 1990 Baltimore Convention Center Baltimore, Maryland

1990 Biophysical Journal  
ofglycerinated insect flight m c e of waterbug Lethocerus show good preervation of crossbridge cture in rigor and relaxed fiber, but leave u ided bow faitflily the variable mix of rigor and relaxed featrs in cotracting  ...  We conclude that cross-linked myosin heads are capable of producing oscillatory power, that process (A) relates to rearrangements of sarcomeres, and that the enhanced oscillatory power is caused by the  ...  It has been proposed that these s ma form metalbinding domains in analogy with the "zinc finger H domains first observed in transcription factor IIIA.  ... 
doi:10.1016/s0006-3495(90)82551-0 fatcat:cxdcxtn5ivfvngrs3w5yuot4om

Development of new strategies for the inhibition of premature labour

Grigsby, Peta Louise, 1975-
Reduced transcriptional activity by dexamethasone has been demonstrated in serum-stimulated fibroblast and mesangial cells stimulated with platelet-derived growth factor (Goppelt-Struebe, 1997) .  ...  These cytokines would then be expected to enhance prostaglandin production by stimulating prostaglandin synthase type-2 (PGHS-2) within the piacental trophoblast (McLaren et aL, 1996) .  ...  Inhibition of premature labor in sheep by a combined treatment of nimesulide, a prostaglandin synthase type 2 inhibitor, and atosiban, an oxytocin receptor antagonist.  ... 
doi:10.4225/03/59d427325b0b3 fatcat:ojrpb52rzbf6toolxvkzawrhga

Responding to restructuring: The geography of trade union responses to the restructuring of local government services in Britain, 1979-89

Joseph Matthew Painter
Intensive research thus involves the use of two types of research: abstract research and co/zcrgre research.  ...  ^Â nd again: All social interaction is situated within time-space boundaries of co-presence (whether or not this be extended via media such as letters, telephone calls etc.).  ...  The notice must state: (i) what work is involved, (ii) when and where a detailed specification can be inspected, (iii) that a copy of the specification may be obtained at a stated price, (iv) that those  ... 
doi:10.21954/ fatcat:cncpfrkdcvamjeyxoa3olpxpai