Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns

(2010) Anton Kratz et al.   BMC GENOMICS

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries

(2010) M. J.L. de Hoon et al.   GENOME RESEARCH

The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells

(2010) Atsutaka Kubosaki et al.   MOLECULAR IMMUNOLOGY

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

(2010) Charles Plessy et al.   NATURE METHODS

SDRF2GRAPH – a visualization tool of a spreadsheet-based description of experimental processes

(2009) Hideya Kawaji et al.   BMC BIOINFORMATICS

Data-driven normalization strategies for high-throughput quantitative RT-PCR

(2009) Jessica C Mar et al.   BMC BIOINFORMATICS

Induction of microRNAs, mir-155, mir-222, mir-424 and mir-503, promotes monocytic differentiation through combinatorial regulation

(2009) A R R Forrest et al.   LEUKEMIA

Tiny RNAs associated with transcription start sites in animals

(2009) Ryan J Taft et al.   NATURE GENETICS

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

MirZ: an integrated microRNA expression atlas and target prediction resource

(2009) J. Hausser et al.   NUCLEIC ACIDS RESEARCH

ENCODE whole-genome data in the UCSC Genome Browser

(2009) K. R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions

(2009) Jessica Severin et al.   GENOME BIOLOGY

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

(2009) Hideya Kawaji et al.   GENOME BIOLOGY

Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation

(2009) Atsutaka Kubosaki et al.   GENOME BIOLOGY

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

(2009) Piotr J Balwierz et al.   GENOME BIOLOGY

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

(2008) E. Valen et al.   GENOME RESEARCH

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression

(2008) H. Parkinson et al.   NUCLEIC ACIDS RESEARCH

The First RSBI (ISA-TAB) Workshop: “Can a Simple Format Work for Complex Studies?”

(2008) Susanna-Assunta Sansone et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY