Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0

Evolutionary Diversification of Duplicated Genes; Experiments B-I, M-P


ABSTRACT: This study measured the rates at which duplicated genes in the Daphnia pulex genome diverge in function, based on significant differences in their gene expression when paralogs of various ages were tested across 8 to 12 contrasting conditions. The conditions were designated A to L. The number and diversity of experiments were designed to uncover condition specific expression. The age of duplicated genes was measured as the level of silent-site nucleotide substitution (Ks) between paralogs. Two methods were used to evaluate the degree to which expression pattern of paralogs differ. (1) The first method investigated variation in the differential expression patterns among duplicates of individual gene families by calculating the M values (log2 treatment – log2 reference) from eight experiments, then calculating Pearson correlations. (2) The second method is a global investigation which defined a distinguishable expression pattern by a significance criterion (p < 0.05) using ANOVA for the simple statistical model of aov( Yab ~ Xab ), for matrices Yab differential expression M values and Xab gene factors, with replicates. We used pr(M) < 0.05 as criterion that expression differs between paralog genes, for zero to twelve treatments. The hypothesis that is tested is one of how many paralog pairs in each Ks category reach the criterion of a distinguishable expression pattern, which is tested for significance with Fisher's exact test for count data. This method is reliable for as few as two probes for one gene and one probe for the other, although a greater number of replicate probes produced more significant results. We compared the gene expression patterns for condition 1 versus condition 2 using four to six biological replicates, including balanced dye-swaps. All probes including random probes were quantile-normalized across chips, subarrays, samples and replicates.

ORGANISM(S): Daphnia pulex

SUBMITTER: Jacqueline Lopez 

PROVIDER: E-GEOD-25843 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

altmetric image

Publications

The ecoresponsive genome of Daphnia pulex.

Colbourne John K JK   Pfrender Michael E ME   Gilbert Donald D   Thomas W Kelley WK   Tucker Abraham A   Oakley Todd H TH   Tokishita Shinichi S   Aerts Andrea A   Arnold Georg J GJ   Basu Malay Kumar MK   Bauer Darren J DJ   Cáceres Carla E CE   Carmel Liran L   Casola Claudio C   Choi Jeong-Hyeon JH   Detter John C JC   Dong Qunfeng Q   Dusheyko Serge S   Eads Brian D BD   Fröhlich Thomas T   Geiler-Samerotte Kerry A KA   Gerlach Daniel D   Hatcher Phil P   Jogdeo Sanjuro S   Krijgsveld Jeroen J   Kriventseva Evgenia V EV   Kültz Dietmar D   Laforsch Christian C   Lindquist Erika E   Lopez Jacqueline J   Manak J Robert JR   Muller Jean J   Pangilinan Jasmyn J   Patwardhan Rupali P RP   Pitluck Samuel S   Pritham Ellen J EJ   Rechtsteiner Andreas A   Rho Mina M   Rogozin Igor B IB   Sakarya Onur O   Salamov Asaf A   Schaack Sarah S   Shapiro Harris H   Shiga Yasuhiro Y   Skalitzky Courtney C   Smith Zachary Z   Souvorov Alexander A   Sung Way W   Tang Zuojian Z   Tsuchiya Dai D   Tu Hank H   Vos Harmjan H   Wang Mei M   Wolf Yuri I YI   Yamagata Hideo H   Yamada Takuji T   Ye Yuzhen Y   Shaw Joseph R JR   Andrews Justen J   Crease Teresa J TJ   Tang Haixu H   Lucas Susan M SM   Robertson Hugh M HM   Bork Peer P   Koonin Eugene V EV   Zdobnov Evgeny M EM   Grigoriev Igor V IV   Lynch Michael M   Boore Jeffrey L JL  

Science (New York, N.Y.) 20110201 6017


We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that  ...[more]

Similar Datasets

2011-02-01 | E-GEOD-25845 | biostudies-arrayexpress
2011-02-01 | E-GEOD-25851 | biostudies-arrayexpress
2011-02-01 | E-GEOD-25850 | biostudies-arrayexpress
2011-02-01 | E-GEOD-25841 | biostudies-arrayexpress
2011-02-01 | GSE25851 | GEO
2011-02-01 | GSE25850 | GEO
2011-02-01 | GSE25841 | GEO
2011-02-01 | GSE25845 | GEO
2011-02-01 | GSE25843 | GEO
2013-03-01 | E-GEOD-43827 | biostudies-arrayexpress