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ModelsDeshpande2019 - Random Forest model to predict long non-coding RNAs from coding RNAs in Zea Mays plant transcriptomic data
This is a Random Forest algorithm-based machine learning model to predict lncRNAs from coding mRNAs in plant transcriptomic data. The model assigns 1 for coding sequences and 2 for long non-coding sequences. The prediction is performed using a combination of Open Reading Frame (ORF) based, Sequence-...
2024-12-09 | BIOMD0000001067 | BioModels
Machine Learning Model FAIR-AIML 
ProteomicsComprehensive Identification of Soybean Long Non-coding RNAs Reveals a Subset of Small Peptide-Coding Transcripts
Long non-coding RNAs (lncRNAs) are defined as non-protein-coding transcripts that are at least 200 nucleotides long. They are known to play pivotal roles in regulating gene expression, especially during stress responses in plants. We used a large collection of in-house transcriptome data from variou...
ORGANISM(S): Glycine max 
2020-01-09 | PXD014553 | Pride
Long non-coding rna Proteomics Soybean Small peptide Transcriptomics 
TranscriptomicsSenescence-associated lncRNAs: senescence-associated long noncoding RNAs.
Noncoding RNAs include small transcripts, such as microRNAs and piwi-interacting RNAs, and a wide range of long noncoding RNAs (lncRNAs). Although many lncRNAs have been identified, only a small number of lncRNAs have been characterized functionally. Here, we sought to identify lncRNAs differentiall...
ORGANISM(S): Homo sapiens 
2016-02-08 | E-GEOD-77675 | biostudies-arrayexpress
TranscriptomicsType I interferon regulates the expression of long non-coding RNAs [RNA-seq]
Interferons (IFNs) are key players in the antiviral response. IFN sensing by the cell activates transcription of IFN-stimulated genes (ISGs) able to induce an antiviral state by affecting viral replication and release. IFN also induces the expression of ISGs that function as negative regulators to l...
ORGANISM(S): Homo sapiens 
2015-01-09 | E-GEOD-64795 | biostudies-arrayexpress
TranscriptomicsTranscriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development [RNA-Seq]
Long non-coding RNAs (lncRNAs) have emerged as critical regulators of gene expression and chromatin modifications, with important functions in development and disease. Here we sought to identify and functionally characterize lncRNAs critical for vascular vertebrate development with significant conse...
ORGANISM(S): Homo sapiens 
2015-05-15 | E-GEOD-54968 | biostudies-arrayexpress
TranscriptomicsControl of Somatic Tissue Differentiation by the Long Non-Coding RNA TINCR (HTS)
Several of the thousands of human long non-coding RNAs (lncRNAs) have been functionally characterized; however, potential roles for lncRNAs in somatic tissue differentiation remain poorly understood. Here we show that a 3.7kb lncRNA, terminal differentiation-induced ncRNA (TINCR), controls human epi...
ORGANISM(S): Homo sapiens 
2012-10-10 | E-GEOD-40121 | biostudies-arrayexpress
TranscriptomicsLong RNA Seq on Sham vs MI Adult Mouse Heart
We systematically identified, annotated and characterised the mouse long non-coding transcriptome during myocardial infarction, revealing hundreds of novel heart specific lncRNAs with unique functional and regulatory characteristics. 2 conditions, 4 biological replicates per condition
ORGANISM(S): Mus musculus 
2014-05-06 | E-GEOD-52313 | biostudies-arrayexpress
TranscriptomicsLong non-coding RNAs regulate adipogenesis (Illumina RNA-Seq)
Adipogenesis involves the regulation of hundreds of genes by several well-studied proteins, but the role of long, noncoding RNAs in this process has not been defined. We track the regulation of hundreds of lncRNAs during adipocyte differentiation, and find several that are essential for this proces...
ORGANISM(S): Mus musculus 
2013-02-15 | E-GEOD-29898 | biostudies-arrayexpress
TranscriptomicsRNA-Seq of human neurons derived from iPS cells Reveals candidate long non-coding RNAs Involved in neurogenesis and neuropsychiatric disorders.
As a preliminary step towards applying next generation sequencing using neurons derived from patient-specific iPSCs, we have carried out an RNA-Seq analysis on control human neurons. Dramatic changes in the expression of coding genes, long non-coding RNAs (lncRNAs), pseudogenes, and splice isoforms ...
ORGANISM(S): Homo sapiens 
2011-10-06 | E-GEOD-32625 | biostudies-arrayexpress
TranscriptomicsLong non-coding RNAs and microRNAs involved in integrated co-regulation of neuronal maturation [mRNA and lncRNA expression]
Neurogenesis is a pro-survival process that comprises of dendritic and axonal growth, synaptogenesis, synaptic and neuronal pruning. These complex processes are determined by temporal gene expression during development, which is in turn tightly regulated by long non-coding RNAs and microRNAs. In thi...
ORGANISM(S): Mus musculus 
2014-10-24 | E-GEOD-44833 | biostudies-arrayexpress
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