Open reading frame (orf)

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Unknown (1455)
Transcriptomics (323)
Genomics (138)
Proteomics (125)
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Models (1)

Organisms

Homo sapiens (144)
Saccharomyces cerevisiae (60)
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Chlorocebus sabaeus (4)
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Escherichia coli str. K-12 substr. MG1655 (4)
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Homo sapiens (25)
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Moraxella catarrhalis (1)
porcine reproductive and respiratory syndrome virus 1 (1)
Caenorhabditis elegans (1)
Drosophila melanogaster (1)
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Arabidopsis thaliana (1)
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Repository

biostudies-arrayexpress (317)
ENA (88)
geo (36)
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pride (34)
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Technology Type

Mass Spectrometry (34)
Shotgun proteomics (19)
Illumina HiSeq 2000 (16)
Affinity purification coupled with mass spectrometry proteomics (8)
Illumina Genome Analyzer II, Illumina HiSeq 2000 (6)
Bottom-up proteomics (5)
Data-dependent acquisition (4)
Gel-based experiment (4)
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Instrument Platform

LTQ Orbitrap Elite (22)
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Not applicable in this study (1)
Thermal cycler (Bio-Rad C1000), Agilent 2100 Bioanalyzer, Qubit 4 Fluorometer (1)
Benchtop centrifuge, vortex, NanoDrop or plate reader (for RiboGreen assay), TapeStation (Agilent) (1)
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418 [Affymetrix] (1)
Illumina Genome Analyzer II (1)
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NextSeq 2000 (1)

Publication Date

2010 (64)
2014 (61)
2013 (36)
2011 (31)
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2012 (27)
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2023 (18)
2016 (16)
2024 (15)
2021 (15)
2020 (15)
2015 (15)
2005 (15)
2026 (14)
2019 (12)
2017 (12)
2008 (12)
2007 (12)
2018 (11)
2022 (10)
2006 (10)
2003 (4)
2004 (3)

UNIPROT ID/AC

10090.ENSMUSP00000021045 (1)
10090.ENSMUSP00000021384 (1)
10090.ENSMUSP00000032399 (1)
10090.ENSMUSP00000034483 (1)
10090.ENSMUSP00000040384 (1)
10090.ENSMUSP00000047171 (1)
10090.ENSMUSP00000048857 (1)
10090.ENSMUSP00000050156 (1)
10090.ENSMUSP00000053997 (1)
10090.ENSMUSP00000057224 (1)
10090.ENSMUSP00000058563 (1)
10090.ENSMUSP00000061247 (1)
10090.ENSMUSP00000062493 (1)
10090.ENSMUSP00000065295 (1)
10090.ENSMUSP00000065508 (1)
10090.ENSMUSP00000066020 (1)
10090.ENSMUSP00000066598 (1)
10090.ENSMUSP00000071284 (1)
10090.ENSMUSP00000071496 (1)
10090.ENSMUSP00000071658 (1)
10090.ENSMUSP00000071763 (1)
10090.ENSMUSP00000072521 (1)
10090.ENSMUSP00000072775 (1)
10090.ENSMUSP00000076447 (1)
10090.ENSMUSP00000078222 (1)
10090.ENSMUSP00000078229 (1)
10090.ENSMUSP00000078239 (1)
10090.ENSMUSP00000078339 (1)
10090.ENSMUSP00000078625 (1)
10090.ENSMUSP00000078670 (1)

ENSEMBL ID

ENSG00000170477 (35)
ENSG00000229353 (19)
ENSG00000147251 (14)
ENSG00000247315 (10)
ENSG00000204131 (8)
ENSG00000214897 (3)
ENSG00000176092 (2)

CHEBI ID

CHEBI:83517 (1)
CHEBI:35331 (1)
CHEBI:8191 (1)
CHEBI:774944 (1)
CHEBI:119569 (1)
CHEBI:309829 (1)
CHEBI:444892 (1)
CHEBI:138738 (1)
CHEBI:83598 (1)
CHEBI:199024 (1)
CHEBI:167309 (1)
CHEBI:86990 (1)
CHEBI:83779 (1)
CHEBI:83829 (1)
CHEBI:83645 (1)
CHEBI:71241 (1)
CHEBI:41275 (1)
CHEBI:83394 (1)
CHEBI:75331 (1)
CHEBI:82040 (1)
CHEBI:81920 (1)
CHEBI:31710 (1)
CHEBI:83533 (1)
CHEBI:52768 (1)
CHEBI:2631 (1)
CHEBI:83465 (1)
CHEBI:83457 (1)
CHEBI:3018 (1)
CHEBI:34648 (1)
CHEBI:81942 (1)

Metabolite Name

Gallamine (1)
Kaempferol-3-O-glucoside (1)
Benzophenone-3 (1)
3-Hydroxy-DL-kynurenine (1)
(+-)-Baclofen (1)
3-Phenoxybenzylalcohol (1)
O-Anisic acid (1)
2-Thiophenecarboxylic acid (1)
Rhodopin (1)
Alpha-keto-glutaric acid (1)
Oxybutynine (1)
Xanthotoxin (1)
Iomeprol (1)
Methomyl (1)
Aminopyrine (1)
N4-Acetylsulfamethazine (1)
Atomoxetine (1)
Acetochlor (1)
1H-indole-3-carboxylic acid (1)
Clopidogrel carboxylic acid (1)
Quinoxyfen (1)
Fenofibrate (1)
Flusilazole (1)
Clofibric acid (1)
Diazoxon (1)
Glycyl-L-proline (1)
Diglyme (1)
D-2-Aminobutyric acid (1)
Pyrazophos (1)
2-Methylindole (1)

First Public Date

2026 (15)
2025 (10)
2023 (9)
2021 (9)
2014 (9)
2022 (6)
2024 (5)
2019 (5)
2016 (5)
2013 (5)
2017 (4)
2020 (3)
2018 (3)

Modelling Approach

Machine learning (1)

Lab affiliation

VIB Midical Biotechnology Center, University of Gent, Belgium (2)
1Department of Pharmacology,Feinberg School of Medicine,Northwestern University, Chicago 2Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University,Northwestern University, Evanston (1)
1Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA 2Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA 3Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA (1)
AG Proteomics & Bioanalytics - Institut für Experimentelle Medizin Christian-Albrechts-Universität zu Kiel 24105 Kiel, Germany (1)
Bioprocessing Technology Institute , Agency for Science, Technology and Research-A*STAR, 20 Biopolis Way 06-01, Singapore 138668, Republic of Singapore (1)
CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia QLD 4067, Australia (1)
Cambridge Institute for Medical Research, Hills Road, Cambridge, CB2 0XY (1)
Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY (1)
Chair, Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida (1)
College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P.R. (1)
Department of Chemistry Chemical Biology Institute (West Campus) Yale University (1)
Department of Environmental and Global Health, College of Public Health and Health Profession, University of Florida, Gainesville, FL (1)
Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany (1)
Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65 Solna, Sweden Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden (1)
Département de Biochimie, Université de Sherbrooke, Québec, Canada (1)
East China Normal University (1)
Forevergen Biosciences Co.,Ltd (1)
Head of Proteomics Research Institute for Systems Biology 401 Terry Ave N, Seattle, WA 98109, USA (1)
Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems,Germany (1)
Institute of Parasitology, Vetsuisse Faculty, University of Berne, Länggass-Strasse 122, CH-3012 Berne, Switzerland (1)
Laboratoire PRISM INSERM U1192 Universite de Lille France (1)
Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192 - Université Lille 1, Bât SN3, 1er étage, Cité Scientifique, F-59655 Villeneuve d’Ascq Cedex (1)
Microbiology, Immunology and Pathology, Lab C210, Colorado State University, United States of America (1)
NISER, Bhubaneswar, India (1)
Prabakaran lab, Department of Genetics, University of Cambridge, United Kingdom (1)
Professor and Head Moritz group, Proteomics lab Institute for systems biology Seattle, WA, USA (1)
Professor in Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Sweden, (1)
Quantitative proteomics University of Tuebingen Auf der Morgenstelle 15 72076 Tuebingen Germany (1)
Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany (1)
Translational Proteomics Laboratory, Institut de recherches cliniques de Montréal (IRCM), Québec, Montréal, Canada. Département de biochimie et médecine moléculaire, Université de Montréal, Québec, Montréal, Canada. (1)

IsPrivate

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Submitter Keywords

FAIR-AIML (1)
Machine Learning Model (1)

Classification

bacteria (5)
viruses (4)
fungi (3)

Study type

Transcription profiling by array (164)
RNA-seq of coding RNA (48)
Unknown experiment type (22)
Other (13)
ChIP-seq (10)
Comparative genomic hybridization by array (9)
Transcription profiling by tiling array (8)
ChIP-chip by tiling array (7)
ChIP-chip by array (6)
RNA-seq of non coding RNA (6)
Ribo-seq (5)
DNA-seq (5)
Proteomic profiling by array (3)
High-throughput sequencing (2)
Transcription profiling by RT-PCR (2)
Transcription profiling by SAGE (1)
Plant - Two-color microarray (1)
Cell line - High-throughput sequencing (1)
Proteomic profiling by mass spectrometer (1)
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Antigen profiling (1)

Release Date

2020 (110)
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2006 (20)
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1997 (4)

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Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides

Computational, genomic, and proteomic approaches have been used to discover nonannotated proteincoding small open reading frames (smORFs). Some novel smORFs have crucial biological roles in cells and organisms, which motivates the search for additional smORFs. Proteomic smORF discovery methods are a...

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

2019-06-26 | MSV000084014 | MassIVE

Transcription profiling by array of post-mortem brain cortex from healthy control patients and amyotrophic lateral sclerosis patients that carry an expanded GGGGCC repeat mutation in the chromosome 9 open reading frame 72 (C9ORF72) gene

The purpose of this experiment was to compare differences in the transcript level between RNA samples collected from post-mortem motor cortex from healthy control patients and amyotrophic lateral sclerosis (ALS) patients that carry an expanded GGGGCC repeat mutation in the chromosome 9 open reading ...

ORGANISM(S): Homo sapiens

2013-10-29 | E-MTAB-1925 | biostudies-arrayexpress

Genome-wide analysis of cellular NMD substrates that regulated by Upf1, PNRC2 or CTIF in HeLa cell

The first round of translation occurs on mRNAs bound by nuclear cap-binding complex (CBC), which is composed of nuclear cap-binding protein (CBP) 80 and 20. During this round of translation, aberrant mRNAs are recognized and downregulated in abundance by nonsense-mediated mRNA decay (NMD), which is ...

ORGANISM(S): Homo sapiens

2012-07-22 | E-GEOD-37538 | biostudies-arrayexpress

Virtual northern using DNA microarrays for genome wide systematic analysis of mRNA lengths, used to measure mRNAs corresponding to 84% of the annotated open reading frames (ORFs) in the yeast genome

We developed a 'Virtual Northern' method, using DNA microarrays for genome-wide systematic analysis of mRNA lengths. We used this method to measure mRNAs corresponding to 84% of the annotated open reading frames (ORFs) in the S. cerevisiae genome, with high precision and accuracy (measurement errors...

ORGANISM(S): Saccharomyces cerevisiae

2005-10-27 | E-SMDB-2508 | biostudies-arrayexpress

K562 polyA RNA-Seq

RNA-Seq reads and TopHat (Trapnell et al. Bioinformatics 2009) alignments of K562 cell-line transcriptome. These were used to validate the expression of short peptides idenitified by Mass-Spectrometry in K562 cells. K562 polyA+ RNA (Batch 1) and total RNA (batch 2) was purchased from Ambion. We use...

ORGANISM(S): Homo sapiens

2012-11-14 | E-GEOD-34740 | biostudies-arrayexpress

Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma

A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation. Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively oncogenic non-canonical open reading frames. To address this question, we performed ribosome profiling of 32 medullob...

EGAS00001007426 | EGA

Identification of small open reading frame encoded peptides of Thermosynechococcus vestitus BP-1(2133)

ORGANISM(S): Thermosynechococcus Elongatus Bp-1

2025-01-09 | PXD059620 |

Identification of small open reading frame encoded peptides of Synechocystis sp. PCC 6803 (6803)

ORGANISM(S): Synechocystis Sp. Pcc 6803 Substr. Kazusa

2025-01-08 | PXD059576 |

Identification of small open reading frame encoded peptides of Picosynechococcus sp. PCC 7002 (7002)

ORGANISM(S): Synechococcus Sp. Pcc 7002

2025-01-10 | PXD059623 |

Identification of small open reading frame encoded peptides of Nostoc sp. PCC 7120 (7120)

ORGANISM(S): Nostoc Sp. Pcc 7120 = Fachb-418

2025-01-09 | PXD059618 |

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