pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes (Q28709088)

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Wen-Kuang Yang

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Hsien-Da Huang

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Jan-Gowth Chang

In-silico human genomics with GeneCards

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language of work or name

English

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publication date

2013

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published in

Database

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volume

2013

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issue

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page(s)

bat001

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cites work

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17 March 2017

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miRBase: integrating microRNA annotation and deep-sequencing data

17 March 2017

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A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

17 March 2017

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Assessing the genomic evidence for conserved transcribed pseudogenes under selection

17 March 2017

1 reference

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Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes

17 March 2017

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Most mammalian mRNAs are conserved targets of microRNAs

17 March 2017

1 reference

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A precisely regulated gene expression cassette potently modulates metastasis and survival in multiple solid cancers

17 March 2017

1 reference

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PseudoGeneQuest - service for identification of different pseudogene types in the human genome

17 March 2017

1 reference

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An endogenous small interfering RNA pathway in Drosophila

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

miRBase: tools for microRNA genomics

17 March 2017

1 reference

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Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures

17 March 2017

1 reference

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MicroRNA targeting specificity in mammals: determinants beyond seed pairing

17 March 2017

1 reference

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Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Strategies for silencing human disease using RNA interference

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

The putatively functional Mkrn1-p1 pseudogene is neither expressed nor imprinted, nor does it regulate its source gene in trans

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

RNAhybrid: microRNA target prediction easy, fast and flexible

17 March 2017

1 reference

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snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

The transcriptional landscape of the mammalian genome

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

HOPPSIGEN: a database of human and mouse processed pseudogenes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Rfam: annotating non-coding RNAs in complete genomes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

17 March 2017

Human MicroRNA targets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Integrative annotation of 21,037 human genes validated by full-length cDNA clones

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

A gene atlas of the mouse and human protein-encoding transcriptomes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

A genome-wide survey of human pseudogenes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Mfold web server for nucleic acid folding and hybridization prediction

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

The human genome browser at UCSC

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Determinator-inhibitor pairs as a mechanism for threshold setting in development: a possible function for pseudogenes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Basic local alignment search tool

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Divergent transcription from active promoters

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

7 April 2017

Vertebrate pseudogenes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

A transcribed pseudogene of MYLK promotes cell proliferation.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

NONCODE v2.0: decoding the non-coding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Alternative splicing events identified in human embryonic stem cells and neural progenitors

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

RNAdb 2.0--an expanded database of mammalian non-coding RNAs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Gene expression omnibus: microarray data storage, submission, retrieval, and analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Genome-wide identification of pseudogenes capable of disease-causing gene conversion.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Evolutionary fate of retroposed gene copies in the human genome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Integrated pseudogene annotation for human chromosome 22: evidence for transcription

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Evolution of nitric oxide synthase regulatory genes by DNA inversion

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567485

Gene expression analyses reveal molecular relationships among 20 regions of the human CNS.

3 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FDATABASE%2FBAT001

Efficient and seamless DNA recombineering using a thymidylate synthase A selection system in Escherichia coli

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FDATABASE%2FBAT001

Identification of miRNomes in Human Liver and Hepatocellular Carcinoma Reveals miR-199a/b-3p as Therapeutic Target for Hepatocellular Carcinoma

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23396300

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Neuronal expression of neural nitric oxide synthase (nNOS) protein is suppressed by an antisense RNA transcribed from an NOS pseudogene

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23396300