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Open Access Research article

Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish

Thilo Borchardt, Mario Looso, Marc Bruckskotten, Patrick Weis, Julia Kruse and Thomas Braun*

Author Affiliations

Max-Planck-Institute for Heart and Lung Research, Parkstr. 1, 61231 Bad Nauheim, Germany

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BMC Genomics 2010, 11:4  doi:10.1186/1471-2164-11-4

Published: 4 January 2010

Additional files

Additional file 1:

2 supplementary figures. Figure S1 shows the read length distribution of 9696 high quality ESTs. Figure S2 shows the length of 2894 contigs and the statistics of ESTs per contig.

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Additional file 2:

Best Blast hits to 1695 contigs with score ≤ 1e-05. Best BLAST hits for each contig were extracted from 5 different BLAST algorithms, sorted by contig ID, BLAST algorithm, and database hit, description and corresponding e-value.

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Additional file 3:

BLAST results of 662 deregulated zebrafish ESTs to the newt heart EST database. 50 zebrafish affymetrix IDs were matched to 46 individual newt contigs with an E-value < 1-05.

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Additional file 4:

Figure S3 shows a graph of GO term nodes used to functionally annotate newt and zebrafish proteins.

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Additional file 5:

Numbers of newt and zebrafish proteins annotated to preselected sub nodes of GO:0008150: biological process. To the GO term sub nodes GO:0008219: cell death, GO:0016477: cell migration, GO:0030154: cell differentiation, GO:0007049: cell cycle, GO:0000278: mitotic cell cycle, GO:0040007: growth, GO:0007275: development, GO:0008283: cell proliferation, GO:0051301: cell division, GO:0007166: cell surface receptor linked signal transduction, GO:0030522: intracellular receptor-mediated signaling pathway, GO:0050851: antigen receptor-mediated signaling pathway, GO:0042060: wound healing, GO:0006936: muscle contraction and GO:0008015: circulation, the number of proteins within daughter nodes was determined for newt and zebrafish and compared to the number of proteins deposited in the GOA database. The ratio of abundance was determined by dividing the number of annotated proteins within a daughter node to the total number of proteins annotated to GO: 0008150: biological process.

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Additional file 6:

Statistical analysis of GO term enrichment. Chi-square test for one to one observations from the newt dataset against the GOA dataset. Level of significance is given as p-value.

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Additional file 7:

List of oligonucleotides used for RT-PCR analysis from regenerating newt hearts.

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Additional file 8:

Figure. Figure S4 demonstrates the features of the newt database.

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