The UCSC Genome Browser Database: update 2006

Hinrichs, Angie S.

doi:10.1093/nar/gkj144

Cited by 1,205 publications

(1,017 citation statements)

References 62 publications

(46 reference statements)

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“…S16). Corresponding to the results of the DMH array, there was a putative CpG island in the miR-135b promoter region 29 ( Supplementary Fig. S17a).…”

Section: Mir-135b Promotes Lung Cancer Cell Growth and Emt In Vitrosupporting

confidence: 62%

MicroRNA-135b promotes lung cancer metastasis by regulating multiple targets in the Hippo pathway and LZTS1

et al. 2013

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Dysregulation of microRNAs has a critical role in cancer progression. Here we identify an intronic microRNA, miR-135b that is upregulated in highly invasive non-small-cell lung cancer cells. Expression of miR-135b enhances cancer cell invasive and migratory abilities in vitro and promotes cancer metastasis in vivo, while specific inhibition of miR-135b by a miR-135b-specific molecular sponge and antagomirs suppresses cancer cell invasion, orthotopic lung tumour growth and metastasis in a mouse model. miR-135b targets multiple key components in the Hippo pathway, including LATS2, b-TrCP and NDR2, as well as LZTS1. Expression of miR-135b, LZTS1, LATS2 and nuclear TAZ predicts poor outcomes of non-small-cell lung cancer. We find that miR-135b is dually regulated by DNA demethylation and nuclear factor-kappaB signalling, implying that abnormal expression of miR-135b in cancer may result from inflammatory and epigenetic modulations. We conclude that miR-135b is an oncogenic microRNA and a potential therapeutic target for non-small-cell lung cancer.

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“…S16). Corresponding to the results of the DMH array, there was a putative CpG island in the miR-135b promoter region 29 ( Supplementary Fig. S17a).…”

Section: Mir-135b Promotes Lung Cancer Cell Growth and Emt In Vitrosupporting

confidence: 62%

MicroRNA-135b promotes lung cancer metastasis by regulating multiple targets in the Hippo pathway and LZTS1

et al. 2013

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“…Putative TATA-boxes were identified, as previously ), using position weight matrices (Bucher 1990); CpG-associated promoters were classified based on the overlap to predicted locations of CpG islands obtained from the UCSC Genome Database (Hinrichs et al 2006) (see Methods). For each promoter type, we analyzed the patterns of indel-purifying selection on the promoter and on their downstream transcripts as before.…”

Section: Conservation Within Macrorna Promotersmentioning

confidence: 99%

“…For this, we did not consider significant sequence similarity to "hypothetical," "unknown," or unnamed sequences as being sufficient evidence for proteincoding sequence, since short open-reading frames are often predicted in transcribed sequence that are not supported by evolutionary conservation in other mammals. (2) It overlaps on the same strand with a transcript of any Ensembl-annotated mouse protein-coding gene (Birney et al 2006) (assembly mm5, obtained from Hinrichs et al 2006). (3) It overlaps on its comple-mentary strand with >20% of its length with the closest transcriptional start or end position of any Ensembl-annotated protein-coding transcript (in the remaining macroRNA set 97% [3030/3122] do not overlap at all).…”

Section: Experimental Data Sourcesmentioning

confidence: 99%

Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs

Ponjavic¹,

Ponting²,

Lunter³

2007

Genome Res.

638

551

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Long transcripts that do not encode protein have only rarely been the subject of experimental scrutiny. Presumably, this is owing to the current lack of evidence of their functionality, thereby leaving an impression that, instead, they represent "transcriptional noise." Here, we describe an analysis of 3122 long and full-length, noncoding RNAs ("macroRNAs") from the mouse, and compare their sequences and their promoters with orthologous sequence from human and from rat. We considered three independent signatures of purifying selection related to substitutions, sequence insertions and deletions, and splicing. We find that the evolution of the set of noncoding RNAs is not consistent with neutralist explanations. Rather, our results indicate that purifying selection has acted on the macroRNAs' promoters, primary sequence, and consensus splice site motifs. Promoters have experienced the greatest elimination of nucleotide substitutions, insertions, and deletions. The proportion of conserved sequence (4.1%-5.5%) in these macroRNAs is comparable to the density of exons within protein-coding transcripts (5.2%). These macroRNAs, taken together, thus possess the imprint of purifying selection, thereby indicating their functionality. Our findings should now provide an incentive for the experimental investigation of these macroRNAs' functions.

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“…Early on in the planning of the ENCODE project, it became apparent that much of the data generated by members of the ENCODE Consortium should be stored in already-existing public repositories in order to maximize the visibility and availability of these data within the biological community. Data that can be directly linked to specific genomic coordinates are available through the UCSC Genome Browser (Hinrichs et al 2006), while array-based data (e.g., expression and chromatin immunoprecipitation [ChIP-chip] data) are deposited in NCBI's Gene Expression Omnibus (GEO) (Barrett et al 2005) or EBI's ArrayExpress (Parkinson et al 2005).…”

mentioning

confidence: 99%

“…These data include mRNA, EST, and STS sequences from GenBank ; single nucleotide polymorphisms stored in NCBI's Database of Single Nucleotide Polymorphisms (dbSNP) ; sequence clusters within the NCBI UniGene database ; diseasecentric information in the Online Mendelian Inheritance in Man (OMIM) database (Hamosh et al 2005); array-based data from NCBI GEO (Barrett et al 2005); and genomic data from the UCSC Genome Browser (Hinrichs et al 2006). While it would be possible to query each of these databases individually, it became obvious that a "portal" was necessary to enable and facilitate the process of gathering all of these disparate types of data from all of these source databases for users interested in either a genomewide or gene-centric perspective of these data.…”

mentioning

confidence: 99%

The ENCODEdb portal: Simplified access to ENCODE Consortium data

Elnitski

Shah²,

Moreland³

et al. 2007

Genome Res.

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The Encyclopedia of DNA Elements (ENCODE) project aims to identify and characterize all functional elements in a representative chromosomal sample comprising 1% of the human genome. Data generated by members of The ENCODE Project Consortium are housed in a number of public databases, such as the UCSC Genome Browser, NCBI's Gene Expression Omnibus (GEO), and EBI's ArrayExpress. As such, it is often difficult for biologists to gather all of the ENCODE data from a particular genomic region of interest and integrate them with relevant information found in other public databases. The ENCODEdb portal was developed to address this problem. ENCODEdb provides a unified, single point-of-access to data generated by the ENCODE Consortium, as well as to data from other source databases that lie within ENCODE regions; this provides the user a complete view of all known data in a particular region of interest. ENCODEdb Genomic Context searches allow for the retrieval of information on functional elements annotated within ENCODE regions, including mRNA, EST, and STS sequences; single nucleotide polymorphisms, and UniGene clusters. Information is also retrieved from GEO, OMIM, and major genome sequence browsers. ENCODEdb Consortium Data searches allow users to perform compound queries on array-based ENCODE data available both from GEO and from the UCSC Genome Browser. Results are retrieved from a specific genomic area of interest and can be further manipulated in a variety of contexts, including the UCSC Genome Browser and the Galaxy large-scale genome analysis platform. The ENCODEdb portal is freely accessible at http://research. nhgri.nih.gov/ENCODEdb.

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The UCSC Genome Browser Database: update 2006

Cited by 1,205 publications

References 62 publications

MicroRNA-135b promotes lung cancer metastasis by regulating multiple targets in the Hippo pathway and LZTS1

MicroRNA-135b promotes lung cancer metastasis by regulating multiple targets in the Hippo pathway and LZTS1

Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs

The ENCODEdb portal: Simplified access to ENCODE Consortium data

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