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. 2011 Jul 21;7(7):e1002119. doi: 10.1371/journal.pcbi.1002119

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Naegle et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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A) The group of phosphopeptides that participate at least 50% of the time in a cluster with enrichment for GO Biological Process term “MAPKKK Cascade”, those proteins with the term are starred. This new group is enriched for GO BP term “positive regulation of DNA replication”. B) These three phosphopeptides always appear when GO Cellular Compartment term “lamellipodium” is enriched, CTTN and PXN are the proteins annotated as being localized in lamellipodium. This new group is enriched for two sequence motifs as well. C) The co-occurrence matrix clustered hieararchically. Co-occurrence between any two phosphopeptides is the number of times those two peptides are clustered together in . For the heat map, the log base 10 was taken of the normalized values, zero values became 0.5/331 prior to log transformation. D) The average values, +/− two standard deviations, are shaded for the three groups highlighted in panel C.

Inline graphic — A) The group of phosphopeptides that participate at least 50% of the time in a cluster with enrichment for GO Biological Process term “MAPKKK Cascade”, those proteins with the term are starred. This new group is enriched for GO BP term “positive regulation of DNA replication”. B) These three phosphopeptides always appear when GO Cellular Compartment term “lamellipodium” is enriched, CTTN and PXN are the proteins annotated as being localized in lamellipodium. This new group is enriched for two sequence motifs as well. C) The co-occurrence matrix clustered hieararchically. Co-occurrence between any two phosphopeptides is the number of times those two peptides are clustered together in . For the heat map, the log base 10 was taken of the normalized values, zero values became 0.5/331 prior to log transformation. D) The average values, +/− two standard deviations, are shaded for the three groups highlighted in panel C.