Reconstructing networks of pathways via significance analysis of their intersections-0

Cant pathways that are respectively overrepresented and underrepresented. Red links indicate pathways interconnections that resulted statistically significant and overrepresented. The largest pathway sub-networks are clearly related to Metabolism, Genetic Information Processing and Signalling biological functions.<p><b>Copyright information:</b></p><p>Taken from "Reconstructing networks of pathways via significance analysis of their intersections"</p><p>http://www.biomedcentral.com/1471-2105/9/S4/S9</p><p>BMC Bioinformatics 2008;9(Suppl 4):S9-S9.</p><p>Published online 25 Apr 2008</p><p>PMCID:PMC2367636.</p><p></p

Reconstructing networks of pathways via significance analysis of their intersections-4

Been removed so that the graph contains only the connected components of Figure 1, evidencing only the significant genes of the significant intersections. Red and blue squares indicate respectively significantly overrepresented and underrepresented pathways whereas the gray indicates not significant pathways. The green tone indicates the degree of pathways membership: from light green (connected to few pathways) to dark green (the hubs).<p><b>Copyright information:</b></p><p>Taken from "Reconstructing networks of pathways via significance analysis of their intersections"</p><p>http://www.biomedcentral.com/1471-2105/9/S4/S9</p><p>BMC Bioinformatics 2008;9(Suppl 4):S9-S9.</p><p>Published online 25 Apr 2008</p><p>PMCID:PMC2367636.</p><p></p

Reconstructing networks of pathways via significance analysis of their intersections-3

3. A) Histogram obtained from the Homo sapiens KEGG database. B) Histogram obtained from the genes on Affymetrix Hgu6800 array. 3) Histogram obtained from the significant genes from AML/ALL dataset.<p><b>Copyright information:</b></p><p>Taken from "Reconstructing networks of pathways via significance analysis of their intersections"</p><p>http://www.biomedcentral.com/1471-2105/9/S4/S9</p><p>BMC Bioinformatics 2008;9(Suppl 4):S9-S9.</p><p>Published online 25 Apr 2008</p><p>PMCID:PMC2367636.</p><p></p

Reconstructing networks of pathways via significance analysis of their intersections-2

Belong to. The majority of genes belong to few pathways whereas few genes (hubs) belong to several pathways (scale free distribution). A) Histogram obtained from the KEGG database for the Rattus norvegicus organism. B) Histogram obtained from the genes on rat Affymetrix U34A Gene Chip. 3) Histogram obtained from the significant genes for MYC dataset.<p><b>Copyright information:</b></p><p>Taken from "Reconstructing networks of pathways via significance analysis of their intersections"</p><p>http://www.biomedcentral.com/1471-2105/9/S4/S9</p><p>BMC Bioinformatics 2008;9(Suppl 4):S9-S9.</p><p>Published online 25 Apr 2008</p><p>PMCID:PMC2367636.</p><p></p

Reconstructing networks of pathways via significance analysis of their intersections-5

Been removed so that the graph contains only the connected components of Figure 2, evidencing only the significant genes of the significant intersections. Red and blue squares indicate respectively significantly overrepresented and underrepresented pathways whereas the gray indicates not significant pathways. The green tone indicates the degree of pathways membership: from light green (connected to few pathways) to dark green (the hubs).<p><b>Copyright information:</b></p><p>Taken from "Reconstructing networks of pathways via significance analysis of their intersections"</p><p>http://www.biomedcentral.com/1471-2105/9/S4/S9</p><p>BMC Bioinformatics 2008;9(Suppl 4):S9-S9.</p><p>Published online 25 Apr 2008</p><p>PMCID:PMC2367636.</p><p></p