18684996
This reference describes Sissrs.
| PMID | PMID 18684996 |
|---|---|
| Title | Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. |
| Year | 2008 |
| Journal | Nucleic Acids Research |
| Author | Jothi R, Cuddapah S, Barski A, Cui K, Zhao K |
| Volume | 36 |
| Start page |
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Full text description
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PMID - 18684996 OWN - NLM STAT - MEDLINE DA - 20080910 DCOM - 20081006 IS - 1362-4962 (Electronic) VI - 36 IP - 16 DP - 2008 Sep TI - Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. PG - 5221-31 AB - ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with ultra high-throughput massively parallel sequencing, is increasingly being used for mapping protein-DNA interactions in-vivo on a genome scale. Typically, short sequence reads from ChIP-Seq are mapped to a reference genome for further analysis. Although genomic regions enriched with mapped reads could be inferred as approximate binding regions, short read lengths (approximately 25-50 nt) pose challenges for determining the exact binding sites within these regions. Here, we present SISSRs (Site Identification from Short Sequence Reads), a novel algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments. The sensitivity and specificity of SISSRs are demonstrated by applying it on ChIP-Seq data for three widely studied and well-characterized human transcription factors: CTCF (CCCTC-binding factor), NRSF (neuron-restrictive silencer factor) and STAT1 (signal transducer and activator of transcription protein 1). We identified 26 814, 5813 and 73 956 binding sites for CTCF, NRSF and STAT1 proteins, respectively, which is 32, 299 and 78% more than that inferred previously for the respective proteins. Motif analysis revealed that an overwhelming majority of the identified binding sites contained the previously established consensus binding sequence for the respective proteins, thus attesting for SISSRs' accuracy. SISSRs' sensitivity and precision facilitated further analyses of ChIP-Seq data revealing interesting insights, which we believe will serve as guidance for designing ChIP-Seq experiments to map in vivo protein-DNA interactions. We also show that tag densities at the binding sites are a good indicator of protein-DNA binding affinity, which could be used to distinguish and characterize strong and weak binding sites. Using tag density as an indicator of DNA-binding affinity, we have identified core residues within the NRSF and CTCF binding sites that are critical for a stronger DNA binding. AD - Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20894, USA. FAU - Jothi, Raja AU - Jothi R FAU - Cuddapah, Suresh AU - Cuddapah S FAU - Barski, Artem AU - Barski A FAU - Cui, Kairong AU - Cui K FAU - Zhao, Keji AU - Zhao K LA - eng PT - Journal Article PT - Research Support, N.I.H., Intramural DEP - 20080806 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (CCCTC-binding factor) RN - 0 (DNA-Binding Proteins) RN - 0 (RE1-silencing transcription factor) RN - 0 (Repressor Proteins) RN - 0 (STAT1 Transcription Factor) RN - 0 (STAT1 protein, human) RN - 0 (Transcription Factors) SB - IM MH - Algorithms MH - Base Sequence MH - Binding Sites MH - *Chromatin Immunoprecipitation MH - DNA-Binding Proteins/*metabolism MH - Genomics/*methods MH - Hela Cells MH - Humans MH - Jurkat Cells MH - Molecular Sequence Data MH - *Regulatory Elements, Transcriptional MH - Repressor Proteins/metabolism MH - STAT1 Transcription Factor/metabolism MH - Transcription Factors/*metabolism PMC - PMC2532738 OID - NLM: PMC2532738 EDAT - 2008/08/08 09:00 MHDA - 2008/10/07 09:00 CRDT - 2008/08/08 09:00 PHST - 2008/08/06 [aheadofprint] AID - gkn488 [pii] AID - 10.1093/nar/gkn488 [doi] PST - ppublish SO - Nucleic Acids Res. 2008 Sep;36(16):5221-31. Epub 2008 Aug 6.
