Human hypothalamic neurons — MKRN3 deficiency
Homo sapiens · Whole hypothalamus · bulk RNA-seq
Selected data and study scope
This dataset contains bulk RNA-seq data from Homo sapiens, sampled from whole hypothalamus. The default comparison examines gene expression in MKRN3 deficient relative to MKRN3 wild type.
The explorer includes 1 track and 1 comparison for this dataset.
The default track, iPSC-derived hypothalamic neurons, includes 3 MKRN3 wild type samples and 3 MKRN3 deficient samples in this comparison. These are analysis sample counts. Check the source for biological replication and pooling.
Interpretation and limitations
These data come from a cell-culture model. Check the cell line or differentiation system and the conditions sampled before interpreting a result.
Expression values are CPM (TMM-normalized): counts per million on library sizes adjusted by the TMM factors of the study’s own edgeR fit. This scale adjusts for library size and composition, not gene length. Use it to inspect a feature across the samples in this analysis. CPM values are not absolute transcript counts.
Evidence and verification
Pipeline QC passed. Human hypothalamic neurons — MKRN3 deficiency; all 1 registered contrasts on default track hypothalamic_neurons
Experimental design passed. Human hypothalamic neurons — MKRN3 deficiency; all 1 registered contrasts on default track hypothalamic_neurons
Author concordance not assessed. Author effect concordance has not been assessed
Pipeline QC can pass while experimental-design limitations remain. Read both assessments before interpreting results.
Open the dataset in the Explorer to read each check and its evidence. Author concordance compares effects for matched genes. It does not require identical author P values or FDR.
Read the analysis methods and interpretation guide and how to cite the source study and HypoExplorer. The source publication may include tissues, groups or comparisons beyond the data shown here.
Source study
Day-30 iPSC-derived hypothalamic-neuron RNA-seq comparing three independent MKRN3-deficient differentiations with three wild-type differentiations. The official Salmon/tximport count estimates are retained without rounding (PMID 37092553; GSE208722)
Source publication
MKRN3 inhibits puberty onset via interaction with IGF2BP1 and regulation of hypothalamic plasticity.
Naulé L, Mancini A, Pereira SA, Gassaway BM, Lydeard JR, Magnotto JC, et al.
JCI insight · 2023
Repository study title
Effect of MKRN3 deletion on gene expression in hypothalamic neurons derived from human induced pluripotent stem cells (hiPSCs)
The original study authors produced these data. HypoExplorer displays selected data and analyses that may cover only part of the study.
Comparisons in HypoExplorer
MKRN3 deficient vs MKRN3 wild type · default
Positive differential-expression values indicate higher expression in the case group relative to the baseline. Check the comparison direction and study design when interpreting results.
Available tracks
| Track | Features | MKRN3 wild type n | MKRN3 deficient n |
|---|---|---|---|
| iPSC-derived hypothalamic neurons | 16,774 | 3 | 3 |
Expression and analysis results
Open this dataset to inspect gene expression and differential-expression results across the available tracks. Pathway enrichment is also available. The pathway databases differ by dataset.
HypoExplorer is in beta testing. Features and analyses may change during testing. Review the original source, analysis methods and quality-control checks before using a result in research.