The Transcriptome of the Sea Urchin Embryo
Manoj P. Samanta1,
Waraporn Tongprasit2,3,
Sorin Istrail4,5,
R. Andrew Cameron5,
Qiang Tu5,
Eric H. Davidson5 and
Viktor Stolc2*
1 Systemix Institute, Los Altos, CA 94024, USA.
2 NASA Ames Genome Research Facility, Moffet Field, CA 94035, USA.
3 Eloret Corporation, Sunnyvale, CA 94086, USA.
4 Brown University, Providence, RI 02912, USA.
5 California Institute of Technology, Pasadena, CA 91125, USA.
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Fig. 1. Visualization of transcription profiles in protein-coding genes and probability of false-positives. (A) An active and an inactive gene. The protein-coding regions of the genes are indicated by the bars, and the orientation of the genes by the DNA strands (W, C) on which they are portrayed. Hybridization of each chip in the array is shown in arbitrary units (ordinate). The active gene is Sp-gcm, for which complete cDNA sequence is also available (21), transcribed from right to left. The activity profile includes the 3'-UTR, extending beyond the terminal codogenic region in the last exon. The inactive gene encodes an adenosine 5'-diphosphate ribosylation factor related protein. The peaks preceding the first exon of gcm, at 26,000 to 28,000, and at 45,000, are of the short noncoding RNA class. (B) Poisson probabilities of occurrence of falsely positive expression assignment, as a function of the total of number of apparently expressed genes. The probability that the expression profile of each gene could have been generated from adventitiously noisy probes was computed as described in the text.
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Fig. 2. Functional distribution of genes expressed in the embryo. The bar chart displays the percentage of annotated genes of different functional categories expressed in the sea urchin embryo. The functional categories are derived from a manual curation database (5) and are shown in table S3. The number at the top of each bar represents the total number of annotated genes in the corresponding category, including all expressed and unexpressed ones. Trans., transcription factors; Signal, signaling genes; Process, basic cellular processes such as metabolism; Cytoskelet., cyto-skeletal; Fertiliz., fertilization; Biominer., biomineralization.
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