Analysis of spatiotemporal specificity of small RNAs regulating hPSC differentiation and beyond
Li, L.; Li, J. F.; Cao, D. D.; Papadopoulos, V.; Chan, W. Y.
Show abstract
We present a quantitative analysis of small RNA dynamics during the transition from hPSCs to the three germ layer lineages to identify spatiotemporal-specific small RNAs that may be involved in hPSC differentiation. To determine the degree of spatiotemporal specificity, we utilized two algorithms, namely normalized maximum timepoint specificity index (NMTSI) and across-tissue specificity index (ASI). NMTSI could identify spatiotemporal-specific small RNAs that go up or down at just one timepoint in a specific lineage. ASI could identify spatiotemporal-specific small RNAs that maintain high expression from intermediate timepoints to the terminal timepoint in a specific lineage. Beyond analyzing single small RNAs, we also quantified the spatiotemporal-specificity of microRNA families and observed their differential expression patterns in certain lineages. To clarify the regulatory effects of group miRNAs on cellular events during lineage differentiation, we performed a gene ontology (GO) analysis on the downstream targets of synergistically up-and downregulated microRNAs. To provide an integrated interface for researchers to access and browse our analysis results, we designed a web-based tool at https://keyminer.pythonanywhere.com/km/.
Matching journals
The top 7 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Single-cell differential splicing analysis reveals high heterogeneity of liver tumor-infiltrating T cells 94%
- CircCNNs, a convolutional neural network framework to better understand the biogenesis of exonic circRNAs 93%
- Pseudotime analysis reveals novel regulatory factors for multigenic onset and monogenic transition of odorant receptor expression 93%
Similar papers in this journal
- A Genome-wide CRISPR screen unveils the endosomal maturation protein WDR91 as a promoter of productive ASO activity in melanoma 93%
- Dynamic regulation of NeuroD1 expression level by a novel viral construct during astrocyte-to-neuron reprogramming 92%
- sTAM: An Online Tool for the Discovery of miRNA-set Level Disease Biomarkers 92%
Similar papers in this journal
- IReNA: integrated regulatory network analysis of single-cell transcriptomes 93%
- Light-Responsive MicroRNAs in Human Retinal Tissue are Differentially Regulated by Distinct Wavelengths of Light 93%
- Cell signaling coordinates global Polycomb Repressive Complex 2 recruitment and gene expression in murine embryonic stem cells 93%