Paquet : pscan-chip (1.1-3)

[ Paquet source : pscan-chip  ]

ChIP-based identifcation of TF binding sites

Regulation of transcription is one of the main check points of gene expression regulation and plays a key role in fundamental processes like cellular differentiation and dynamic molecular responses to stimuli The transcriptional activity of genes is finely regulated by the interaction of sequence elements on the DNA (transcription factor binding sites or TFBSs) and particular proteins called Transcription Factors (TFs).

TFBSs are usually clustered in specific regulatory genomic regions called promoters and enhancers. TFs usually recognize TFBSs in a loose sequence specific fashion but there is no computational way to determine if any given sequence motif on the DNA is actually bound in-vivo by a TF, even when the motif is an istance of the sequences typically bound by the TF itself.

Tools like Pscan and PscanChIP analyse a set of regulatory sequences to detect motif enrichment. The rationale is that if a given TFBS is present in a "surpisingly high" number of istances then there is a good chance that the TF that recognize that motif is a common regulator of the input sequences, thus they use redundancy as an information source.

While Pscan (of the pscan-tfbs package) is tailored to work on promoters, that is the regulatory regions upstream of transcription start sites, PscanChIP is suited to work on more general regulatory genomic regions like the ones identified through ChIP-Seq experiments.

Autres paquets associés à pscan-chip

• dep: libc6 (>= 2.29)

  bibliothèque C GNU : bibliothèques partagées
  un paquet virtuel est également fourni par libc6-udeb

• dep: libgcc-s1 (>= 3.0) [non armel, armhf]

  bibliothèque de prise en charge de GCC

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

• dep: libgsl25 (>= 2.6)

  GNU Scientific Library (GSL) -- library package

• dep: libstdc++6 (>= 5.2)

  bibliothèque standard C++ de GNU v3

• rec: pscan-chip-data

  auxiliary data for PScan-ChIP

• sug: pscan-tfbs

  search for transcription factor binding sites

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Architecture	Taille du paquet	Espace occupé une fois installé	Fichiers
amd64	83,6 ko	188,0 ko	[liste des fichiers]
arm64	78,5 ko	164,0 ko	[liste des fichiers]
armel	78,9 ko	162,0 ko	[liste des fichiers]
armhf	78,4 ko	134,0 ko	[liste des fichiers]
i386	87,1 ko	186,0 ko	[liste des fichiers]
mips64el	84,0 ko	199,0 ko	[liste des fichiers]
mipsel	84,5 ko	192,0 ko	[liste des fichiers]
ppc64el	85,4 ko	248,0 ko	[liste des fichiers]
s390x	79,4 ko	180,0 ko	[liste des fichiers]