A search engine to identify pathway genes from expression data on multiple organisms-4

<p><b>Copyright information:</b></p><p>Taken from "A search engine to identify pathway genes from expression data on multiple organisms"</p><p>http://www.biomedcentral.com/1752-0509/1/20</p><p>BMC Systems Biology 2007;1():20-20.</p><p>Published online 4 May 2007</p><p>PMCID:PMC1878502.</p><p></p>of recall. The results obtained for individual PMT nodes are shown as separate lines with single-organism results shown as dashed lines and multiple-organism node results shown as solid lines. Average precisions for , , Eukaryote, and Cellular nodes are not shown because each had fewer than 10 pathways with the minimum number of query genes. The highest precision level at 50% recall rate for all single-organism nodes versus multiple-organism nodes. Each dot corresponds to the precision obtained by the search-engine for a single pathway. Solid line indicates , the line of equal performance; multiple-organism searches resulted in higher precision for pathways above the line and a lower precision for pathways below the line. Dashed lines indicate a high precision rate of 20%

A search engine to identify pathway genes from expression data on multiple organisms-3

<p><b>Copyright information:</b></p><p>Taken from "A search engine to identify pathway genes from expression data on multiple organisms"</p><p>http://www.biomedcentral.com/1752-0509/1/20</p><p>BMC Systems Biology 2007;1():20-20.</p><p>Published online 4 May 2007</p><p>PMCID:PMC1878502.</p><p></p>ar position in the search ordering. A rank-ratio of 0.10 is equivalent to the 90percentile; a rank-ratio of 0.01 is equivalent to 99percentile. Bars correspond to GenMAPP pathways run through single-species PMT nodes (dark gray) or multiple-species ancestral PMT nodes (black) and to random pathways run through single-species nodes (white) or multiple-species ancestral nodes (light gray)

A search engine to identify pathway genes from expression data on multiple organisms-5

<p><b>Copyright information:</b></p><p>Taken from "A search engine to identify pathway genes from expression data on multiple organisms"</p><p>http://www.biomedcentral.com/1752-0509/1/20</p><p>BMC Systems Biology 2007;1():20-20.</p><p>Published online 4 May 2007</p><p>PMCID:PMC1878502.</p><p></p> precision of at least 20% in one or more nodes of the PMT at the 50% recall rate. Yellow corresponds to high precisions near 100%, and blue to low precisions near 0%. The first 21 rows (Multi) correspond to pathways for which a precision of at least 20% was achieved only by a multiple-organism node. The next 14 rows (Multi & Single) correspond to pathways for which both multiple- and single-organism nodes achieved a precision of at least 20%; the last five rows (Single) correspond to pathways for which only a single-organism node achieved a precision of at least 20%. Superscript letters indicate the database from which pathways were collected: K, KEGG [14]; G, GO [13]; M, GenMAPP [12]; B, BioCarta [34]. Superscript numbers indicate pathway names that were abbreviated: 1, ; 2, ; 3, ; 4, ; 5,

Basic characteristics of study subjects.

<p>Basic characteristics of study subjects.</p

Genotypic and allelic associations of <i>GAPDH</i> variants with PD.

<p>^a Adjusted by Bonferroni correction for multiple testing.</p><p>Genotypic and allelic associations of <i>GAPDH</i> variants with PD.</p

Comparison of our rotenone ST models with other models.

<p>Data on the rotenone ST and SYS administration models are from our study and other studies, while data on the MPTP models are all from reports by others. Animal, animal used for the research; Instrument, special instrument or routes of administration; Nutritional status, the nutritional status of PD animal models and whether supplementation is required; Peripheral toxicity, peripheral organ toxicity caused by the neurotoxin; Application, whether the model is suitable for the study of pathogenesis, pathophysiological research, or drug screening of PD; Slow progression, idiopathic PD-like slow progression; Selective degeneration, selective degeneration of DA neurons; Long-term progression, long-term (more than three months) progression without intervention; Extensive involvement, ability to reproduce extensive pathological involvement observed in PD patients; Cost, costs of neurotoxin drugs, instruments, nutritional supplementation (ST, Stereotaxical Infusion; SYS, Systemic administration; S.C., subcutaneous injection).</p

Pathological changes in peripheral organs in Parkinsonian rats.

<p>A: The alveolar walls of the ST infusion rats were thin and delicate; B: neutrophilic exudates were detected in the pulmonary alveoli; C: the normal hepatic lobules and central veins; D: the central vein of the hepatic lobule was fractured in SYS rats; E and H: the normal renal glomerulus and renal medulla; F and I: Red blood cells were increased in the renal glomeruli and renal medulla; J: the normal white pulp of the spleen; K: hemorrhage and hemosiderin deposition in the spleen of the SYS rats; L and M: normal heart and stomach of SYS rats (Scale bars = 50 µm).</p

Differential effect of APO on the ST infusion rats.

<p>The APO-induced rotations were counted on the 1^st, 2^nd, 3^rd, 4^th, 6^th, 8^th, 10^th, 12^th, 16^th, 20^th, and 24^th weeks following the 3-µg rotenone infusion and on the 2^nd, 3^rd, 4^th, 6^th, and 8^th weeks following the 6-µg and 12-µg rotenone infusions. The control animals did not exhibit rotations. The total number of rotations is expressed as the mean±SD (n = 6).</p

Effect of rotenone on the striatum, VTA, and SNc TH immunoreactivity.

<p>Pictures of the TH immunostaining of coronal sections were taken at the level of the striatum from the DMSO- or rotenone-infused rats (3-µg group) four weeks after infusion. Each treatment group had four rats. The left striatum represents the intact side of the brain, and the right striatum represents the lesioned side of the same animal. The TH immunoreactivity on the ipsilateral side of the striatum was decreased by 66.4% (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007878#pone-0007878-g004" target="_blank">Figure 4I–J</a>; *P<0.05, as compared to the contralateral side). The ST-infused rats (3- and 12-µg groups) and SYS models were sacrificed four weeks after the rotenone infusion, and coronal sections were HE-stained and immunohistochemically stained with TH. HE-staining showed a significant decrease in the number of neurons in the VTA and SNc (A, 3 µg group). The number of TH-positive neurons (E) was decreased by 43.7% (B), 53.6% (C), 59.0%, and 75.8% (D) in the right side of the 3- and 12-µg ST models and in the left and right sides of SYS models, respectively, as compared to the contralateral side of the ST models. The integrated intensity of the VTA and SNc was decreased by 38.1%, 54.5%, 46.4%, and 95.3% in the right side of the 3- and 12-µg ST models and in the left and right sides of the SYS models, respectively (F) (*P<0.05, as compared with the contralateral side; #P<0.05, as compared with the lesioned side of 3-µg group; and P<0.05, as compared with the other side of the SYS group) (Scale bars = 50 µm).</p

Changes in striatal levels of DA and 5-HT after rotenone infusion.

<p>For the dose-response (3-, 6-, 12-µg groups) studies, the animals were sacrificed at the fourth week following the ST infusion of rotenone, and the (A) DA and (C) 5-HT contents were measured. For the time-response studies, the animals were infused with 3 µg of rotenone and sacrificed on the second, fourth, sixth, and eighth week (B and D). The results are expressed in ng/mg (wet tissue), and the data were given as the mean±SD (n = 6). *P<0.05 as compared to contralateral side.</p