The Major histocompatibility complex (MHC) on human chromosome 6 has paralogy regions on chromosomes 1, 9 and 19. Much of the human genome seems to be assignable to paralogy regions.
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The Major histocompatibility complex (MHC) on human chromosome 6 has paralogy regions on chromosomes 1, 9 and 19. Much of the human genome seems to be assignable to paralogy regions.
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First, gene mapping data in humans and mice revealed extensive paralogy regions - sets of genes on one chromosome related to sets of genes on another chromosome in the same species, indicative of duplication events in evolution. Paralogy regions were generally in sets of four. Second, cloning of Hox genes in lancelet revealed presence of a single Hox gene cluster, in contrast to the four clusters in humans and mice. Data from additional gene families revealed a common one-to-many rule when lancelet and vertebrate genes were compared.
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In this process, the annotation sharing score was calculated using GeneDecks Partner Hunter (now called Genes Like Me) to give paralogy. Inactivation targets were be extracted after the microarray experiments of resistant and non-resistant neuroblastoma cell lines.
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Superfamily members may be in different species, with the ancestral protein being the form of the protein that existed in the ancestral species (orthology). Conversely, the proteins may be in the same species, but evolved from a single protein whose gene was duplicated in the genome (paralogy).
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The widespread adoption of performance reviews, organizational assessments, and learning outcomes by different social institutions worldwide has led social researchers to theorize "audit culture" and "global performativity". Against performativity and Jurgen Habermas' call for consensus, Lyotard argued for legitimation by paralogy, or the destabilizing, often paradoxical, introduction of difference into language games.
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This was suggested to be inconsistent with the 2R hypothesis. However, other researchers have argued that such 'topology tests' do not test 2R rigorously, because recombination could have occurred between the closely related chromosomes generated by polyploidy, because inappropriate genes had been compared and because different predictions are made if genome duplication occurred through hybridisation between species. In addition, several researchers were able to date duplications of gene families within paralogy regions consistently to the early evolution of vertebrates, after divergence from amphioxus, consistent with the 2R hypothesis. When complete genome sequences became available for vertebrates, Ciona intestinalis and lancelets, it was found that much of the human genome was arranged in paralogy regions that could be traced to large-scale duplications, and that these duplications occurred after vertebrates had diverged from tunicates and lancelets.
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Sometimes, large regions of chromosomes share gene content similar to other chromosomal regions within the same genome. They are well characterised in the human genome, where they have been used as evidence to support the 2R hypothesis. Sets of duplicated, triplicated and quadruplicated genes, with the related genes on different chromosomes, are deduced to be remnants from genome or chromosomal duplications. A set of paralogy regions is together called a paralogon. Well- studied sets of paralogy regions include regions of human chromosome 2, 7, 12 and 17 containing Hox gene clusters, collagen genes, keratin genes and other duplicated genes, regions of human chromosomes 4, 5, 8 and 10 containing neuropeptide receptor genes, NK class homeobox genes and many more gene families, and parts of human chromosomes 13, 4, 5 and X containing the ParaHox genes and their neighbors.
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Taken together, these two lines of evidence suggest that two genome duplications occurred in the ancestry of vertebrates, after it had diverged from the cephalochordate evolutionary lineage. Pattern predicted for the relative locations of paralogous genes from two genome duplications Controversy about the 2R hypothesis hinged on the nature of paralogy regions. It is not disputed that human chromosomes bear sets of genes related to sets of genes on other chromosomes; the controversy centres on whether they were generated by large-scale duplications that doubled all the genes at the same time, or whether a series of individual gene duplications occurred followed by chromosomal rearrangement to shuffle sets of genes together. Hughes and colleagues found that phylogenetic trees built from different gene families within paralogy regions had different shapes, suggesting that the gene families had different evolutionary histories.
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Power Graph Analysis has been shown to be useful for the analysis of several types of biological networks such as Protein-protein interaction networks, domain-peptide binding motifs, Gene regulatory networks and Homology/Paralogy networks. Also a network of significant disease-trait pairs have been recently visualized and analyzed with Power Graphs. Network compression, a new measure derived from Power Graphs, has been proposed as a quality measure for protein interaction networks.
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Orthology or paralogy inference requires an assessment of sequence homology, usually via sequence alignment. Phylogenetic analyses and sequence alignment are often considered jointly, as phylogenetic analyses using DNA or RNA require sequence alignment and alignments themselves often represent some hypothesis of homology. As proper ortholog identification is pivotal to phylogenetic analyses, there are a variety of methods available to infer orthologs and paralogs. These methods are generally distinguished as either graph-based algorithms or tree-based algorithms.
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PhylomeDB is a public biological database for complete catalogs of gene phylogenies (phylomes). It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions which are based on the analysis of the phylogenetic trees. The automated pipeline used to reconstruct trees aims at providing a high-quality phylogenetic analysis of different genomes, including Maximum Likelihood tree inference, alignment trimming and evolutionary model testing.
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However, models have limits and need to be used cautiously. For instance, the conflicting phylogenies can be the result of events not accounted for by the model, such as unrecognized paralogy due to duplication followed by gene losses. Also, many approaches rely on a reference species tree that is supposed to be known, when in many instances it can be difficult to obtain a reliable tree. Finally, the computational costs of reconstructing many gene/species trees can be prohibitively expensive.
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As discussed in more detail below, phylogenetic methods range from simple methods merely identifying discordance between gene and species trees to mechanistic models inferring probable sequences of HGT events. An intermediate strategy entails deconstructing the gene tree into smaller parts until each matches the species tree (genome spectral approaches). Explicit phylogenetic methods rely upon the accuracy of the input rooted gene and species trees, yet these can be challenging to build. Even when there is no doubt in the input trees, the conflicting phylogenies can be the result of evolutionary processes other than HGT, such as duplications and losses, causing these methods to erroneously infer HGT events when paralogy is the correct explanation.
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Zerknüllt (zen, German for "crumpled") is a gene in the Antennapedia complex of Drosophila (fruit flies) and other insects, where it operates very differently from the canonical Hox genes in the same gene cluster. Comparison of Hox genes between species showed that the Zerknüllt gene evolved from one of the standard Hox genes (the 'paralogy group 3' Hox gene) in insects through accumulating many amino acid changes, changing expression pattern, losing ancestral function and gaining a new function. Zerknüllt codes for a homeoprotein regulates aspects of early embryogenesis in insects. Unlike the canonical Hox genes which are expressed in precise zones along the anteroposterior (head to tail) body axis, zerknüllt expression is restricted along the dorsoventral (back to belly) body axis.
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In English names for fields of study, the suffix -logy is most frequently found preceded by the euphonic connective vowel o so that the word ends in -ology.Eric Partridge, Origins, 2nd edition, New York, Macmillan, 1959 In these Greek words, the root is always a noun and -o- is the combining vowel for all declensions of Greek nouns. However, when new names for fields of study are coined in modern English, the formations ending in -logy almost always add an -o-, except when the root word ends in an "l" or a vowel, as in these exceptions:Words Ending In ogy : Words Ending With ogy analogy, dekalogy, disanalogy, genealogy, genethlialogy, herbalogy (a variant of herbology), mammalogy, mineralogy, paralogy, petralogy (a variant of petrology); elogy; antilogy, festilogy; trilogy, tetralogy, pentalogy; palillogy, pyroballogy; dyslogy; eulogy; and brachylogy. Linguists sometimes jokingly refer to haplology as haplogy (subjecting the word haplology to the process of haplology itself).
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