Posts Tagged ‘gencode’

BMC Genomics | Full text | Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential

Friday, July 31st, 2015

[440 @GencodeGenes] #Pseudogenes transcribed in breast…carcinoma show subtype-specific expression & ceRNA potential

Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila

Wednesday, March 11th, 2015

Published Online December 10 2009

Science DOI: 10.1126/science.1181421


Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila

Sergei Nechaev1,
David C. Fargo2,
Gilberto dos Santos1,
Liwen Liu3,
Yuan Gao4 and
Karen Adelman1,*

The landscape of long noncoding RNAs in the human transcriptome : Nature Genetics : Nature Publishing Group

Wednesday, January 28th, 2015

Landscape of lncRNAs in the human #transcriptome Derived from RNAseq read assembly; not much overlap w/ @GencodeGenes

Matthew K Iyer,
Yashar S Niknafs,
Rohit Malik,
Udit Singhal,
Anirban Sahu,
Yasuyuki Hosono,
Terrence R Barrette,
John R Prensner,
Joseph R Evans,
Shuang Zhao,
Anton Poliakov,
Xuhong Cao,
Saravana M Dhanasekaran,
Yi-Mi Wu,
Dan R Robinson,
David G Beer,
Felix Y Feng,
Hariharan K Iyer
& Arul M Chinnaiyan

Nature Genetics (2015) doi:10.1038/ng.3192Received 20 June 2014 Accepted 18 December 2014

A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics | eLife

Sunday, June 22nd, 2014

We identify an lncRNA pseudogene, Lethe (named after the mythological river of forgetfulness, for its role in negative feedback), which is expressed in response to proinflammatory cytokines TNFα and IL-1β, and the anti-inflammatory agent, dexamthasone, but is not responsive to microbial components, and is primarily found on the chromatin. Lethe is regulated by RelA, independent of pseudogene family members and proximal genes. Additionally, Lethe is dramatically downregulated in aged spleen. Finally, Lethe binds directly to RelA to inhibit NF-κB DNA binding activity. These findings suggest that Lethe may function as a novel negative regulator of NF-κB, to help fine tune the inflammatory response.

A mammalian #pseudogene #lncRNA at the interface of inflammation… Lethe may down-regulate NF-kB via binding to RelA

No use of Gencode pgenes !

Encode-annotation interesting paper

Monday, April 14th, 2014

recent publication from the Donnelly group comparing using GENCODE or Refeq annotation when predicting variants effects.
Choice of transcripts and software has a large effect on variant annotation
Genome Medicine 2014, 6:26 doi:10.1186/gm543