GeneProf
GeneProf Data is an open web resource for analysed functional genomics experiments. We have built up a large collection of completely processed RNA-seq and ChIP-seq studies by carefully and transparently reanalysing and annotating high-profile public data sets. GeneProf makes these data instantly accessible in an easily interpretable, searchable and reusable manner and thus opens up the path to the advantages and insights gained from genome-scale experiments to a broader scientific audience. Moreover, GeneProf supports programmatic access to these data via web services to further facilitate the reuse of experimental data across tools and laboratories.
Description
More detailed information about this field from each metasource.
GeneProf Data is an open web resource for analysed functional genomics experiments. We have built up a large collection of completely processed RNA-seq and ChIP-seq studies by carefully and transparently reanalysing and annotating high-profile public data sets. GeneProf makes these data instantly accessible in an easily interpretable, searchable and reusable manner and thus opens up the path to the advantages and insights gained from genome-scale experiments to a broader scientific audience. Moreover, GeneProf supports programmatic access to these data via web services to further facilitate the reuse of experimental data across tools and laboratories.
metasource: Fairsharing.orgversion: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Webpage:
http://www.geneprof.orgWebpage
More detailed information about this field from each metasource.
http://www.geneprof.org
metasource: Fairsharing.orgversion: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
GeneProf: analysis of high-throughput sequencing experiments
PMID: 22205509
metasource: Fairsharing.org
version: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gkt966
metasource: Fairsharing.org
version: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Publications
More detailed information about this field from each metasource.
GeneProf: analysis of high-throughput sequencing experiments
PMID: 22205509
metasource: Fairsharing.org
version: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gkt966
metasource: Fairsharing.orgversion: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
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GeneProf: analysis of high-throughput sequencing experiments
PubMed citations: 49.
49 articles citing: GeneProf: analysis of high-throughput sequencing experiments
Segmentation and Modelling of the Nuclear Envelope of HeLa Cells Imaged with Serial Block Face Scanning Electron Microscopy. PMID:34460669
RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis. PMID:34082707
DolphinNext: a distributed data processing platform for high throughput genomics. PMID:32306927
HaTSPiL: A modular pipeline for high-throughput sequencing data analysis. PMID:31613890
Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation. PMID:30275266
Live cell imaging of X chromosome reactivation during somatic cell reprogramming. PMID:30094351
Functional characteristics of novel pancreatic Pax6 regulatory elements. PMID:30007277
Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche. PMID:29950724
Depletion of Mediator Kinase Module Subunits Represses Superenhancer-Associated Genes in Colon Cancer Cells. PMID:29507187
Distinct SoxB1 networks are required for naïve and primed pluripotency. PMID:29256862
A molecular roadmap of the AGM region reveals BMPER as a novel regulator of HSC maturation. PMID:29093060
Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling. PMID:28981893
Ageing and hypoxia cause protein aggregation in mitochondria. PMID:28644434
RNAseq Reveals Complex Response of Campylobacter jejuni to Ovine Bile and In vivo Gallbladder Environment. PMID:28611744
Genome-wide Methyl-Seq analysis of blood-brain targets of glucocorticoid exposure. PMID:28557603
GeMSTONE: orchestrated prioritization of human germline mutations in the cloud. PMID:28521008
ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data. PMID:28402545
Two factor-based reprogramming of rodent and human fibroblasts into Schwann cells. PMID:28169300
Mitotic binding of Esrrb marks key regulatory regions of the pluripotency network. PMID:27723719
Identification of key player genes in gene regulatory networks. PMID:27599550
Structure and function of the bacterial decapping enzyme NudC. PMID:27428510
Computational challenges in modeling gene regulatory events. PMID:27390891
Defining the Clinical Value of a Genomic Diagnosis in the Era of Next-Generation Sequencing. PMID:27362341
SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis. PMID:27255077
Transcriptomic Signature of the SHATTERPROOF2 Expression Domain Reveals the Meristematic Nature of Arabidopsis Gynoecial Medial Domain. PMID:26983993
Regulation of Budding Yeast CENP-A levels Prevents Misincorporation at Promoter Nucleosomes and Transcriptional Defects. PMID:26982580
An interactive environment for agile analysis and visualization of ChIP-sequencing data. PMID:26926434
SPARC-Dependent Cardiomyopathy in Drosophila. PMID:26839388
SREBP and MDT-15 protect C. elegans from glucose-induced accelerated aging by preventing accumulation of saturated fat. PMID:26637528
Genome-wide endogenous DAF-16/FOXO recruitment dynamics during lowered insulin signalling in C. elegans. PMID:26539642
Independent evidence for an association between general cognitive ability and a genetic locus for educational attainment. PMID:25951819
NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs. PMID:25533955
A Three-Gene Assay for Monitoring Immune Quiescence in Kidney Transplantation. PMID:25429124
Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells. PMID:25428352
Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems. PMID:25364758
Small RNAs as important regulators for the hybrid vigour of super-hybrid rice. PMID:25129133
Cyclin-dependent kinase 8 module expression profiling reveals requirement of mediator subunits 12 and 13 for transcription of Serpent-dependent innate immunity genes in Drosophila. PMID:24778181
eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing. PMID:24593312
Circadian behavior is light-reprogrammed by plastic DNA methylation. PMID:24531307
HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis. PMID:24475057
GeneProf data: a resource of curated, integrated and reusable high-throughput genomics experiments. PMID:24174536
DEXUS: identifying differential expression in RNA-Seq studies with unknown conditions. PMID:24049071
PhagoSight: an open-source MATLAB® package for the analysis of fluorescent neutrophil and macrophage migration in a zebrafish model. PMID:24023630
A direct physical interaction between Nanog and Sox2 regulates embryonic stem cell self-renewal. PMID:23892456
NGS-Trex: Next Generation Sequencing Transcriptome profile explorer. PMID:23815181
The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability. PMID:23793381
High-resolution analysis with novel cell-surface markers identifies routes to iPS cells. PMID:23728301
Esrrb is a direct Nanog target gene that can substitute for Nanog function in pluripotent cells. PMID:23040477
Next-generation sequencing data interpretation: enhancing reproducibility and accessibility. PMID:22898652 - http://dx.doi.org/10.1093/nar/gkt966
Tags:
Tags
More detailed information about this field from each metasource.
binding site
metasource: Fairsharing.org
version: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
chromatin immunoprecipitation - dna microarray
metasource: Fairsharing.org
version: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
chromatin immunoprecipitation - dna sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
computational predictions
metasource: Fairsharing.org
version: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene expression data
metasource: Fairsharing.org
version: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene model annotation
metasource: Fairsharing.org
version: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
rna sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
ribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Tags
More detailed information about this field from each metasource.
binding site
metasource: Fairsharing.orgversion: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
chromatin immunoprecipitation - dna microarray
metasource: Fairsharing.orgversion: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
chromatin immunoprecipitation - dna sequencing
metasource: Fairsharing.orgversion: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
computational predictions
metasource: Fairsharing.orgversion: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene expression data
metasource: Fairsharing.orgversion: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene model annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
rna sequencing
metasource: Fairsharing.orgversion: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
ribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: GeneProf; GeneProf; DOI: https://doi.org/10.25504/FAIRsharing.qmygaa; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
binding site chromatin immunoprecipitation - dna microarray chromatin immunoprecipitation - dna sequencing computational predictions gene expression gene model annotation rna sequence rna
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