Cattle hypothalamus — short-term diet restriction
Bos taurus · Whole hypothalamus · bulk RNA-seq
Selected data and study scope
This dataset contains bulk RNA-seq data from Bos taurus, sampled from whole hypothalamus. The default comparison examines gene expression in Restricted-diet anovulatory relative to Higher-feed ovulatory control.
The explorer includes 1 track and 1 comparison for this dataset.
The default track, Whole hypothalamus, includes 7 Higher-feed ovulatory control samples and 7 Restricted-diet anovulatory samples in this comparison. These are analysis sample counts. Check the source for biological replication and pooling.
Interpretation and limitations
The measurement combines expression from the cells in the tissue sample. A difference in tissue expression alone does not identify which cell type contributes to it.
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. Cattle hypothalamus — short-term diet restriction; all 1 registered contrasts on default track hypothalamus
Experimental design review needed. Cattle hypothalamus — short-term diet restriction; all 1 registered contrasts on default track hypothalamus
Author concordance review needed. Selected author genes only; restricted_anovulatory_vs_control. P values and FDR are contextual. Numerical acceptance: strong correlation and matched-gene direction.
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
Hypothalamus RNA-seq comparing seven restricted-diet anovulatory with seven higher-feed ovulatory control heifers. Seven restricted-diet ovulatory animals form a distinct third arm and are excluded; official per-sample HTSeq integer counts are modeled by edgeR-QL (PMID 29121875; GSE49540)
Source publication
Matthews D, Diskin MG, Kenny DA, Creevey CJ, Keogh K, Waters SM
BMC genomics · 2017
Repository study title
Effect of short term diet restriction on gene expression in the bovine hypothalamus using next generation RNA sequencing technology
The original study authors produced these data. HypoExplorer displays selected data and analyses that may cover only part of the study.
Comparisons in HypoExplorer
Restricted-diet anovulatory vs Higher-feed ovulatory control · 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 | Higher-feed ovulatory control n | Restricted-diet anovulatory n |
|---|---|---|---|
| Whole hypothalamus | 11,831 | 7 | 7 |
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.