Syntenic correlation indices.

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+[[!meta title="Measures of synteny conservation between species pairs."]]
+[[!tag synteny method]]
+
+Housworth EA, Postlethwait J
+
+Genetics. 2002 Sep;162(1):441-8. doi:10.1093/genetics/162.1.441
+
+Measures of synteny conservation between species pairs.
+
+[[!pmid 12242252 desc="Introduces a syntenic correlation measure, ρ, which is a
+scaled chi-square statistic, and an alternative measure λ with measures “the
+proportion of errors made in assigning a gene to a chromosome in one species
+that can be eliminated by knowing which chromosome the orthologue belongs to in
+the other species.”"]]
+
+“_We introduce a measure of genomic conservation, which we call syntenic
+correlation, which corresponds to a measure of how far the orthologues are from
+being independently scattered in the genomes of the two species. This measure
+is standardized to be between zero, for completely randomized arrangements of
+orthologues between the genomes, and one, for two genomes with perfect synteny
+conservation. Further, this measure can be used to compare genomic distances
+(i.e., Oxford grids) between many pairs of species._”
+

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@@ -84,6 +84,12 @@ Squid chromosomes still have synteny with scallop, but gene order is scrambled
    orthologue co-occurs close by in the other genome. It varies between 0 (no
    co-occurrence) and 1 (complete gene order conservation)”.
 
+ - [[Housworth and Postlethwait, 2002|biblio/12242252]] defined the syntenic
+   correlation measure ρ, based on chi-square and an alternative λ not based on
+   chi-square.  Both attempt to estimate how wrong we would be to hypothesise
+   that a given gene has its orthologue in a homologous chromosome of a related
+   species.
+
  - “Chains” and “nets” of pairwise alignements between two genomes are described
    in [[Kent and coll, 2003|biblio/14500911]].