Searching journal content for articles similar to Keller et al. 18 (5): 706.

Displaying results 1-10 of 19

For checked items

view abstracts
download to citation manager

Select this article
Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...and AI Institute, Johns Hopkins University, Baltimore, Maryland 21218, USA Corresponding author: ajbattle@jhu.eduAbstractGene coexpression networks (GCNs) describe relationships among genes that maintain cellular identity and homeostasis. However, typical RNA-seq experiments often lack sufficient sample...
OPEN ACCESS ARTICLE
Select this article
Method: A best-match approach for gene set analyses in embedding spaces
- Lechuan Li,
- Ruth Dannenfelser,
- Charlie Cruz,
- and Vicky Yao
Genome Res. September 2024 34: 1421-1433; Published in Advance September 4, 2024, doi:10.1101/gr.279141.124
...capture additional, complementary information with respect to gene functional similarity. Furthermore, because ubiquitously expressed genes can give rise to different disease-susceptibility and phenotypes in different tissues (Hekselman and Yeger-Lotem 2020), using tissue-specific network models as input...
OPEN ACCESS ARTICLE
Select this article
Research: Variation in histone configurations correlates with gene expression across nine inbred strains of mice
- Anna L Tyler,
- Catrina Spruce,
- Romy Kursawe,
- Annat Haber,
- Robyn L Ball,
- Wendy A Pitman,
- Alexander D Fine,
- Narayanan Raghupathy,
- Michael Walker,
- Vivek M Philip,
- Christopher L Baker,
- J. Matthew Mahoney,
- Gary A. Churchill,
- Jennifer J Trowbridge,
- Michael L Stitzel,
- Kenneth Paigen,
- Petko M Petkov,
- and Gregory W Carter
Genome Res. May 22, 2023 gr.277467.122; Published in Advance May 22, 2023, doi:10.1101/gr.277467.122
...been well documented, their epigenetic14 diversity has not. Epigenetic modifications, such as histone modifications and DNA methylation,15 are important regulators of gene expression, and as such are a critical mechanistic link between16 genotype and phenotype. Therefore, creating a map of epigenetic...
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Research: Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation
- Montgomery Blencowe,
- Xuqi Chen,
- Yutian Zhao,
- Yuichiro Itoh,
- Caden N. McQuillen,
- Yanjie Han,
- Benjamin L. Shou,
- Rebecca McClusky,
- Karen Reue,
- Arthur P. Arnold,
- and Xia Yang
Genome Res. May 2022 32: 807-824; Published in Advance April 8, 2022, doi:10.1101/gr.275965.121
...specificity was prominent, with a major impact of estradiol on adipose tissue gene regulation and of testosterone on the liver transcriptome. The networks affected by the three sex-biasing factors include development, immunity and metabolism, and tissue-specific regulators were identified for these networks...
OPEN ACCESS ARTICLE
Select this article
Research: Natural variation of histone modification and its impact on gene expression in the rat genome
- Carola Rintisch,
- Matthias Heinig,
- Anja Bauerfeind,
- Sebastian Schafer,
- Christin Mieth,
- Giannino Patone,
- Oliver Hummel,
- Wei Chen,
- Stuart Cook,
- Edwin Cuppen,
- Maria Colomé-Tatché,
- Frank Johannes,
- Ritsert C. Jansen,
- Helen Neil,
- Michel Werner,
- Michal Pravenec,
- Martin Vingron,
- and Norbert Hubner
Genome Res. June 2014 24: 942-953; Published in Advance May 2, 2014, doi:10.1101/gr.169029.113
...to be coregulated by the QTL hotspot at chromosome 3 (Fig. 3F). Using the congenic rats, we confirmed 768 (85%) of the trans-linked H3K4me3 marks, and interestingly, higher histone modification levels were always associated with the BN allele, indicating a common regulation of these marks. Genes corresponding...
Select this article
Methods: Integrating siRNA and protein–protein interaction data to identify an expanded insulin signaling network
- Zhidong Tu,
- Carmen Argmann,
- Kenny K. Wong,
- Lyndon J. Mitnaul,
- Stephen Edwards,
- Iliana C. Sach,
- Jun Zhu,
- and Eric E. Schadt
Genome Res. June 2009 19: 1057-1067; Published in Advance March 4, 2009, doi:10.1101/gr.087890.108
..., beyond those genes represented in the siRNA hit list. This is achieved by integrating known pathway relationships and experimentally determined protein–protein interactions to link true positive siRNA hits to networks of genes related to insulin signaling. Our analysis results in the identification...
Select this article
Methods: Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network
- Ivan Iossifov,
- Tian Zheng,
- Miron Baron,
- T. Conrad Gilliam,
- and Andrey Rzhetsky
Genome Res. July 2008 18: 1150-1162; Published in Advance April 16, 2008, doi:10.1101/gr.075622.107
...it is that a particular gene is linked to a phenotype given that the phenotype is unlinked to any position in the . We need this test because genes within a large molecular network differ markedly in their topological neighborhoods; the highly connected genes tend to be spuriously implicated in linkage to a phenotype...
OPEN ACCESS ARTICLE
Select this article
Research: A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort
- Danielle M. Greenawalt,
- Radu Dobrin,
- Eugene Chudin,
- Ida J. Hatoum,
- Christine Suver,
- John Beaulaurier,
- Bin Zhang,
- Victor Castro,
- Jun Zhu,
- Solveig K. Sieberts,
- Susanna Wang,
- Cliona Molony,
- Steven B. Heymsfield,
- Daniel M. Kemp,
- Marc L. Reitman,
- Pek Yee Lum,
- Eric E. Schadt,
- and Lee M. Kaplan
Genome Res. July 2011 21: 1008-1016; Published in Advance May 20, 2011, doi:10.1101/gr.112821.110
...correlated. In both tissues the gene set correlated to preop BMI at FDR <5% was enriched for genes present in the macrophage enriched metabolic network (MEMN; E = 7.59 3 10#2;32), which has been linked to obesity previously (Chen et al. 2008; Emilsson et al. 2008). TIMP4 is a metallopeptidase inhibitor...
Select this article
Research: LCM-seq reveals unique transcriptional adaptation mechanisms of resistant neurons and identifies protective pathways in spinal muscular atrophy
- Susanne Nichterwitz,
- Jik Nijssen,
- Helena Storvall,
- Christoph Schweingruber,
- Laura Helen Comley,
- Ilary Allodi,
- Mirjam van der Lee,
- Qiaolin Deng,
- Rickard Sandberg,
- and Eva Hedlund
Genome Res. August 2020 30: 1083-1096; Published in Advance August 20, 2020, doi:10.1101/gr.265017.120
...the transcriptional dynamics in discrete neuronal populations using laser capture microdissection coupled with RNA sequencing (LCM-seq). Using gene correlation network analysis, we reveal a TRP53-mediated stress response that is intrinsic to all somatic motor neurons independent of their vulnerability, but absent...
OPEN ACCESS ARTICLE
Select this article
Research: Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
- Irene Mei,
- Susanne Nichterwitz,
- Melanie Leboeuf,
- Jik Nijssen,
- Isadora Lenoel,
- Dirk Repsilber,
- Christian S. Lobsiger,
- and Eva Hedlund
Genome Res. September 2025 35: 1975-1991; Published in Advance July 17, 2025, doi:10.1101/gr.279501.124
...as Islet 1), peripherin (Prph), and neurofilament, heavy polypeptide (Nefh). CN12 and spinal MNs also expressed Isl2 and Mnx1, whereas those markers were nearly absent in CN3/4 and visceral CN10 MNs (Supplemental Fig. S2C). Principal component analysis (PCA) including all expressed genes showed...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Keller et al. 18 (5): 706.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: