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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...correlation coefficient higher than 0.7. (D) Heatmap showing the normalized expression level detected in RNA sequencing data sets for host and nested gene pairs with a Spearman's rank correlation coefficient higher than 0.7. Host genes were clustered using hierarchical clustering according to their expression...
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Resource: Multiscale network modeling reveals the gene regulatory landscape driving cancer prognosis in 32 cancer types
- Peng Xu and
- Bin Zhang
Genome Res. October 2023 33: 1806-1817; Published in Advance October 31, 2023, doi:10.1101/gr.278063.123
...by interactions between gene expression and methylation. Coregulated genes of network modules were enriched in chromosome cytobands and preferentially localized in open chromatin regions. The preserved network modules formed 330 module clusters that resided in chromosome hot spots. The cancer...
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LETTER: An analysis of the gene complement of a marsupial, Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes
- Leo Goodstadt,
- Andreas Heger,
- Caleb Webber,
- and Chris P. Ponting
Genome Res. July 2007 17: 969-981; Published in Advance May 10, 2007, doi:10.1101/gr.6093907
...lipocalin cluster is orthologous to developmentally regulated milk protein genes in the tammar wallaby ( Trott et al. 2002 ). Beta-microseminoprotein, an abundant constituent of seminal plasma, has been duplicated extensively in the Monodelphis lineage, resulting in 12 copies, whereas all other mammals...
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LETTER: Large-Scale Protein Annotation through Gene Ontology
- Hanqing Xie,
- Alon Wasserman,
- Zurit Levine,
- Amit Novik,
- Vladimir Grebinskiy,
- Avi Shoshan,
- and Liat Mintz
Genome Res. May 1, 2002 12: 785-794; doi:10.1101/gr.86902
.... , Noonan J.P. , Zhang M.Q. , Myers R.M. , et al. ( 2001 ) Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Genome Res. 11 : 389 – 404 . ↵ Yona G. , Linial N. , Linial M. ( 1999 ) ProtoMap: Automatic classification of protein sequences, a hierarchy of protein families...
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LETTER: Genome-wide patterns of gene flow across a house mouse hybrid zone
- Katherine C. Teeter,
- Bret A. Payseur,
- Leslie W. Harris,
- Margaret A. Bakewell,
- Lisa M. Thibodeau,
- Janelle E. O’Brien,
- James G. Krenz,
- Maria A. Sans-Fuentes,
- Michael W. Nachman,
- and Priscilla K. Tucker
Genome Res. January 2008 18: 67-76; Published in Advance November 19, 2007, doi:10.1101/gr.6757907
.... There is a cluster of 60 protocadherin genes located 5–15 Mb upstream of marker 18.028, which has a cline width of 135.4 km. These genes are not in the 10-Mb windows, which accounts for the difference in the trends between the 10-Mb and 30-Mb analyses. Finally, mesoderm development showed a nonsignificant trend...
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Research: High-throughput mapping of the promoters of the mouse olfactory receptor genes reveals a new type of mammalian promoter and provides insight into olfactory receptor gene regulation
- E. Josephine Clowney,
- Angeliki Magklara,
- Bradley M. Colquitt,
- Nidhi Pathak,
- Robert P. Lane,
- and Stavros Lomvardas
Genome Res. August 2011 21: 1249-1259; Published in Advance June 24, 2011, doi:10.1101/gr.120162.110
...biological functions and do not share recent common ancestry. Even when Olfactory Receptor genes are excluded from this list, the majority of these genes are organized in genomic clusters characterized by significant copy number variation and polymorphism (Supplemental Table S2; Wong et al. 2007; Liu et al...
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LETTER: Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire
- Ali Mortazavi,
- Evonne Chen Leeper Thompson,
- Sarah T. Garcia,
- Richard M. Myers,
- and Barbara Wold
Genome Res. October 2006 16: 1208-1221; Published in Advance September 8, 2006, doi:10.1101/gr.4997306
...,” are conspicuously absent from the other NRSE cohorts. On detailed inspection, the latter results are mainly due to NRSE1 matches within the paralogous protocadherin β cluster. This calls attention to a specific interpretation issue in GO enrichment analysis, which is the power of very similar paralogs in gene...
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LETTER: The Binding Sites for the Chromatin Insulator Protein CTCF Map to DNA Methylation-Free Domains Genome-Wide
- Rituparna Mukhopadhyay,
- WenQiang Yu,
- Joanne Whitehead,
- JunWang Xu,
- Magda Lezcano,
- Svetlana Pack,
- Chandrasekhar Kanduri,
- Meena Kanduri,
- Vasudeva Ginjala,
- Alexander Vostrov,
- Wolfgang Quitschke,
- Igor Chernukhin,
- Elena Klenova,
- Victor Lobanenkov,
- and Rolf Ohlsson
Genome Res. August 2004 14: 1594-1602; Published in Advance July 15, 2004, doi:10.1101/gr.2408304
...with -wide epigenetic states. The projects have revealed that most, if not all mammalian genes are organized in clusters. This organization presumably reflects the need to initiate and maintain proper expression domains that exploit common cis -regulatory elements in lineage-specific manners. Yet...
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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
...-tuning of differences between cell populations. For instance, we found that in the brain, the astrocyte and oligodendrocyte lineages clearly differ by gene expression, but at the splicing level, oligodendrocyte precursor cells cluster with astrocytes rather than committed and mature oligodendrocytes (Joglekar et al...
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ARTICLE: Coelacanth genome sequence reveals the evolutionary history of vertebrate genes
- James P. Noonan,
- Jane Grimwood,
- Joshua Danke,
- Jeremy Schmutz,
- Mark Dickson,
- Chris T. Amemiya,
- and Richard M. Myers
Genome Res. December 2004 14: 2397-2405; Published in Advance November 15, 2004, doi:10.1101/gr.2972804
...., and Myers, R.M. 2004 . Gene conversion and the evolution of protocadherin gene cluster diversity. Genome Res. 14 : 354 -366. ↵ Ohno, S. 1970 . Evolution by gene duplication . Springer-Verlag, Berlin, Germany. ↵ Postlethwait, J.H., Yan, Y.L., Gates, M.A., Horne, S., Amores, A., Brownlie, A., Donovan, A...

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