Page Comparison

R 2.13.0, SageBionetworksCoex 0.11, running time \~4.5 hours
!CorHeatmap.jpg|thumbnail!  !GeneDendrogram.jpg|thumbnail! !ScaleFree.jpg|thumbnail!
Total number of modules is 9
|| Module || \# of loci ||
| black | 32 |
| blue | 264 |
| brown | 243 |
| green | 39 |
| pink | 32 |
| red | 35 |
| turquoise | 1422 |
| yellow | 159 |

Analysis of the PC1 of each module:
!PercentVarianceExplained_Eigen1.png|thumbnail!  !Eigen1_variablity.png|thumbnail!

Chromosomal density maps can be found [here|^Histogram_chromosomal_distr.pdf]

Only brown and green modules are represented by CpG mostly coming from a single chromosome (chromosome X and chromosome 1)

Gene Ontology analysis:
{csv:heading=0}yellow,BP,2.67E-04,2.51,11.41,24,1375,intracellular signal transduction,3.77E-01
yellow,MF,7.36E-04,77.52,0.04,2,5,somatostatin receptor activity,2.58E-01
yellow,CC,8.66E-04,18.62,0.19,3,21,lateral plasma membrane,1.60E-01
yellow,BP,9.51E-04,2.27,12.44,24,1499,regulation of response to stimulus,1.00E+00
turquoise,CC,1.11E-32,2.66,849.87,1008,9154,intracellular,7.13E-30
turquoise,CC,1.21E-32,2.18,642.09,829,6916,membrane-bounded organelle,7.79E-30
turquoise,CC,1.35E-32,2.17,641.16,828,6906,intracellular membrane-bounded organelle,8.68E-30
turquoise,CC,5.76E-31,2.21,707.92,884,7625,intracellular organelle,3.71E-28
turquoise,CC,7.46E-31,2.20,709.40,885,7641,organelle,4.80E-28
turquoise,CC,8.34E-31,2.50,832.97,990,8972,intracellular part,5.37E-28
turquoise,CC,8.57E-21,1.79,410.27,557,4419,intracellular organelle part,5.52E-18
turquoise,CC,4.34E-20,1.77,415.74,560,4478,organelle part,2.80E-17
turquoise,CC,2.25E-17,1.92,172.69,276,1860,intracellular organelle lumen,1.45E-14
turquoise,CC,6.95E-17,1.90,176.58,279,1902,organelle lumen,4.48E-14
red,MF,1.35E-04,5.25,8.74,18,4231,catalytic activity,2.00E-02
red,MF,9.14E-04,6.43,1.19,6,577,oxidoreductase activity,1.35E-01
pink,MF,2.71E-04,102.96,0.02,2,17,sialyltransferase activity,2.44E-02
green,BP,1.03E-61,23614.73,0.07,23,34,keratinization,6.17E-60
green,BP,2.87E-52,5755.11,0.14,23,68,keratinocyte differentiation,1.72E-50
green,BP,3.42E-50,4460.02,0.17,23,81,epidermal cell differentiation,2.05E-48
green,BP,1.00E-40,1524.71,0.40,23,191,epithelial cell differentiation,6.02E-39
green,BP,3.09E-40,1446.01,0.42,23,200,epidermis development,1.85E-38
green,BP,4.39E-34,746.28,0.76,23,361,epithelium development,2.64E-32
green,BP,5.42E-26,312.07,1.69,23,799,tissue development,3.25E-24
green,BP,1.44E-18,134.49,3.55,23,1674,organ development,8.64E-17
green,BP,7.25E-18,123.65,3.80,23,1796,cell differentiation,4.35E-16
green,BP,1.25E-17,120.18,3.90,23,1839,cellular developmental process,7.49E-16
brown,CC,4.76E-05,2.03,80.75,104,6916,membrane-bounded organelle,1.19E-02
brown,CC,9.01E-05,1.97,80.63,103,6906,intracellular membrane-bounded organelle,2.25E-02
brown,MF,1.44E-04,Inf,0.02,2,2,glutamate dehydrogenase activity,5.99E-02
brown,MF,1.44E-04,Inf,0.02,2,2,glutamate dehydrogenase [NAD(P)+] activity,5.99E-02
brown,MF,1.44E-04,Inf,0.02,2,2,"oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor",5.99E-02
brown,MF,1.44E-04,Inf,0.02,2,2,leucine binding,5.99E-02
brown,BP,2.31E-04,15.64,0.31,4,25,central nervous system neuron development,3.74E-01
brown,MF,2.63E-04,31.39,0.13,3,11,guanylate kinase activity,1.09E-01
brown,CC,3.35E-04,1.91,89.21,109,7641,organelle,8.37E-02
brown,CC,4.48E-04,3.08,4.96,14,425,nucleolus,1.12E-01
blue,BP,8.17E-12,4.07,12.53,41,755,neurogenesis,2.14E-08
blue,BP,4.57E-11,3.08,25.39,60,1530,cell communication,1.20E-07
blue,CC,5.95E-11,2.59,51.42,94,3146,plasma membrane,1.80E-08
blue,BP,9.63E-11,3.93,11.83,38,713,generation of neurons,2.52E-07
blue,CC,1.47E-10,2.53,52.23,94,3195,cell periphery,4.45E-08
blue,BP,1.93E-10,3.20,20.13,51,1213,nervous system development,5.04E-07
blue,BP,9.59E-10,3.53,13.41,39,808,cell-cell signaling,2.51E-06
blue,BP,1.08E-09,3.78,11.13,35,671,neuron differentiation,2.82E-06
blue,BP,5.93E-09,2.35,69.28,108,4175,multicellular organismal process,1.55E-05
blue,BP,2.62E-08,2.54,29.80,60,1796,cell differentiation,6.85E-05
black,MF,5.63E-04,68.90,0.04,2,23,myosin binding,7.26E-02
{csv}