Editor\u27s Notes, Chiba Medical Journal 90-1

Multiple sequence alignment of deduced amino acid sequences of 25 wheat annexin genes with rice annexin OsAnn2 (Os05g31760) obtained by ClustalW. (PDF 212 kb

Three mostly used linkage criteria for the hierarchical clustering.

<p>To calculate the pairwise distances for the hierarchical clustering, three commonly used linkage criteria were taken from the Wikipedia (<a href="http://en.wikipedia.org/wiki/Hierarchical_clustering" target="_blank">http://en.wikipedia.org/wiki/Hierarchical_clustering</a>).</p><p>Three mostly used linkage criteria for the hierarchical clustering.</p

The summarization of the methods for illustrating heatmaps among the 202 papers published in 2012 on five leading journals.

a<p>Tools, the name of used tools;</p>b<p>Num., the number of papers that used the tool;</p>c<p>Web link, the website of the tool;</p>d<p>N/A, not mentioned in the corresponding papers.</p><p>The summarization of the methods for illustrating heatmaps among the 202 papers published in 2012 on five leading journals.</p

Illustrating heatmaps by HemI 1.0.

<p>(A) Thermal shifts, which indicate binding affinities of 185 compounds to 13 PARPs, were measured by DSF. A higher value represents a stronger binding affinity. (B) Totally, 428 androgen-repressed genes were identified from LNCaP cells, after the treatment of 1 nM synthetic androgen R1881 for 3, 6, 12, 24 and 48 hours. Values shown were normalized to 0 hour and log² transformed.</p

Using frequency of heatmap.

<p>To estimate <i>how</i> many papers contain heatmaps, we went through all original research papers (excluding reviews and other articles) published in 2012 of five leading journals as below.</p>a<p>Num. of Heatmaps, the number of papers containing with at least one heatmap figure;</p>b<p>Per., the percentiles.</p><p>Using frequency of heatmap.</p

Seven distances for the clustering.

<p>To calculate the distances for the hierarchical and k-means clustering approaches, up to 7 mostly used distances were adopted.</p><p>Seven distances for the clustering.</p

Usage of HemI 1.0.

<p>(A) The numerical data in one of three file formats can be directly loaded, whereas the data area can be selected by dragging or holding-SHIFT-then-click manipulations. Titles for <i>X</i>-axis or <i>Y</i>-axis can also be specified; (B) Multiple options for manipulating the heatmp; (C) The numeric data can be clustered for either or both of <i>X</i>-axis and <i>Y</i>-axis; (D) Publication-quality figures can be exported, and two figure formats were supported.</p

Comparison of obesity indexes according to dietary choline (mg/kg/day) intake¹.

<p>Comparison of obesity indexes according to dietary choline (mg/kg/day) intake<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155403#t005fn001" target="_blank">¹</a>.</p

Correlations between dietary choline and betaine intakes (mg/kg/day) with body composition¹.

<p>Correlations between dietary choline and betaine intakes (mg/kg/day) with body composition<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155403#t002fn001" target="_blank">¹</a>.</p

THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy

<p>Macroautophagy/autophagy is a highly conserved process for degrading cytoplasmic contents, determines cell survival or death, and regulates the cellular homeostasis. Besides ATG proteins, numerous regulators together with various post-translational modifications (PTMs) are also involved in autophagy. In this work, we collected 4,237 experimentally identified proteins regulated in autophagy and cell death pathways from the literature. Then we computationally identified potential orthologs of known proteins, and developed a comprehensive database of The Autophagy, Necrosis, ApopTosis OrchestratorS (THANATOS, <a href="http://thanatos.biocuckoo.org" target="_blank">http://thanatos.biocuckoo.org</a>), containing 191,543 proteins potentially associated with autophagy and cell death pathways in 164 eukaryotes. We performed an evolutionary analysis of <i>ATG</i> genes, and observed that ATGs required for the autophagosome formation are highly conserved across eukaryotes. Further analyses revealed that known cancer genes and drug targets were overrepresented in human autophagy proteins, which were significantly associated in a number of signaling pathways and human diseases. By reconstructing a human kinase-substrate phosphorylation network for ATG proteins, our results confirmed that phosphorylation play a critical role in regulating autophagy. In total, we mapped 65,015 known sites of 11 types of PTMs to collected proteins, and revealed that all types of PTM substrates were enriched in human autophagy. In addition, we observed multiple types of PTM regulators such as protein kinases and ubiquitin E3 ligases or adaptors were significantly associated with human autophagy, and again the results emphasized the importance of PTM regulations in autophagy. We anticipated THANATOS can be a useful resource for further studies.</p