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h3.


h3. Network and network diagnostics with M value based data (center, batch, plate row and column variables removed)

R version 2.13.0 64 bit, SageBionetworksCoex 0.11, running time \~4.5 hours (~27k by 486)

 !CorHeatmap.jpg|thumbnail!   !ScaleFree.jpg|thumbnail! !GeneDendrogram.jpg|thumbnail!

beta=6, R=0.89. Number of modules: 18 + 1 (grey):
|| Module || \# of probes || Module || \# of probes ||
| black | 108 | pink | 97 |
| blue | 1206 | purple | 89 |
| brown | 615 | red | 113 |
| cyan | 43 | salmon | 46 |
| greenyellow | 86 | tan | 85 |
| grey | 22115 | turquoise | 2151 |
| grey60 | 33 | yellow | 469 |
| lightcyan | 34 | lightgreen | 32 |
| magenta | 92 | green | 121 |
| midnightblue | 43 | | |
Analysis of the first PC of each module:

!Eigen1_variablity.png|thumbnail! !PercentVarianceExplained_Eigen1.png|thumbnail!

With M value almost no modules were composed of the CpGs from a single chromosome (chromosomal density plots can be found [here|^Histogram_chromosomal_distr.pdf])

Modules lightcyan, lightgreen, salmon and yellow, >55% of the loci came from the same chromosome (plots are [here|^GeneModuleDistrib.pdf])

Gene Ontology analyses of each module (top 10 categories were selected and KEGG pathways didn't work for my on that day):
{csv}black,CC,1.09E-10,5.64,8.61,30,1621,extracellular region,1.16E-08
black,MF,1.81E-06,11.25,0.85,8,161,sugar binding,3.11E-04
black,BP,7.73E-06,6.91,1.75,10,354,innate immune response,6.83E-03
black,BP,1.63E-05,4.62,3.82,14,772,defense response,1.44E-02
black,BP,2.40E-05,Inf,0.01,2,2,virion transport,2.12E-02
black,BP,2.40E-05,Inf,0.01,2,2,intracellular virion transport,2.12E-02
black,MF,4.32E-05,6.20,1.70,9,323,carbohydrate binding,7.43E-03
black,MF,5.97E-05,4.87,2.68,11,510,calcium ion binding,1.03E-02
black,BP,7.18E-05,417.48,0.01,2,3,peptide antigen transport,6.34E-02
black,BP,8.37E-05,4.14,3.86,13,780,immune response,7.40E-02
blue, CC,1.86E-10,1.76,128.76,196,1855,plasma membrane part,8.71E-08
blue,CC,3.93E-09,1.56,218.36,292,3146,plasma membrane,1.85E-06
blue,CC,8.56E-09,1.54,221.76,294,3195,cell periphery,4.01E-06
blue,CC,2.36E-08,1.82,76.42,124,1101,intrinsic to plasma membrane,1.11E-05
blue,CC,6.28E-08,1.79,75.31,121,1085,integral to plasma membrane,2.95E-05
blue,BP,1.31E-07,1.98,48.18,85,707,cell adhesion,5.39E-04
blue,BP,1.31E-07,1.98,48.18,85,707,biological adhesion,5.39E-04
blue,CC,2.05E-07,1.43,390.92,463,5632,membrane,9.62E-05
blue,BP,4.90E-07,6.13,3.34,15,49,cellular defense response,2.02E-03
blue,CC,2.19E-06,3.05,10.69,28,154,anchoring junction,1.03E-03
brown,CC,4.68E-14,2.46,380.34,449,9154,intracellular,2.24E-11
brown,CC,2.12E-13,2.00,286.94,366,6906,intracellular membrane-bounded organelle,1.01E-10
brown,CC,2.78E-13,1.99,287.35,366,6916,membrane-bounded organelle,1.33E-10
brown,CC,5.90E-13,2.29,372.78,440,8972,intracellular part,2.83E-10
brown,CC,9.12E-12,1.95,316.81,388,7625,intracellular organelle,4.37E-09
brown,CC,1.37E-11,1.94,317.48,388,7641,organelle,6.56E-09
brown,CC,1.98E-10,1.77,183.61,252,4419,intracellular organelle part,9.47E-08
brown,CC,8.68E-10,1.73,186.06,252,4478,organelle part,4.16E-07
brown,CC,1.63E-09,1.94,77.28,128,1860,intracellular organelle lumen,7.78E-07
brown,CC,5.39E-09,1.88,80.40,130,1935,membrane-enclosed lumen,2.58E-06
cyan,CC,1.79E-04,3.62,7.06,17,2371,protein complex,2.34E-02
cyan,BP,3.41E-04,4.60,2.87,10,985,transcription from RNA polymerase II promoter,2.91E-01
cyan,BP,4.45E-04,80.91,0.03,2,11,protein destabilization,3.81E-01
cyan,BP,4.45E-04,80.91,0.03,2,11,"regulation of DNA damage response, signal transduction by p53 class mediator",3.81E-01
cyan,BP,4.54E-04,5.65,21.11,30,7248,metabolic process,3.88E-01
cyan,BP,5.53E-04,5.78,1.49,7,510,cellular protein localization,4.73E-01
cyan,BP,5.54E-04,8.55,0.69,5,236,nucleocytoplasmic transport,4.74E-01
cyan,BP,5.66E-04,5.75,1.49,7,512,cellular macromolecule localization,4.84E-01
cyan,BP,5.76E-04,8.48,0.69,5,238,nuclear transport,4.92E-01
cyan,BP,6.88E-04,19.72,0.17,3,60,positive regulation of cell cycle arrest,5.88E-01
green,BP,3.91E-48,628.02,0.20,24,34,keratinization,2.66E-45
green,BP,2.67E-40,155.30,0.40,25,68,keratinocyte differentiation,1.81E-37
green,BP,5.06E-38,119.11,0.48,25,81,epidermal cell differentiation,3.44E-35
green,BP,8.57E-28,39.79,1.13,25,191,epithelial cell differentiation,5.82E-25
green,BP,2.83E-27,37.71,1.18,25,200,epidermis development,1.92E-24
green,BP,8.30E-21,19.36,2.13,25,361,epithelium development,5.64E-18
green,MF,3.13E-15,80.06,0.20,10,42,olfactory receptor activity,4.57E-13
green,BP,2.40E-14,46.87,0.34,11,58,sensory perception of smell,1.63E-11
green,BP,1.09E-12,8.07,4.73,25,799,tissue development,7.41E-10
green,BP,1.67E-12,6.56,24.69,53,4175,multicellular organismal process,1.13E-09
greenyellow,CC,2.07E-13,69.55,0.20,9,38,keratin filament,2.73E-11
greenyellow,CC,8.79E-12,25.43,0.57,11,111,intermediate filament,1.16E-09
greenyellow,CC,8.87E-11,20.14,0.71,11,137,intermediate filament cytoskeleton,1.17E-08
greenyellow,MF,2.18E-06,5.93,2.72,13,518,structural molecule activity,5.10E-04
greenyellow,BP,8.41E-06,9.05,1.04,8,200,epidermis development,8.91E-03
greenyellow,BP,4.76E-05,8.34,0.97,7,186,visual perception,5.05E-02
greenyellow,BP,4.76E-05,8.34,0.97,7,186,sensory perception of light stimulus,5.05E-02
greenyellow,MF,8.89E-05,42.64,0.09,3,17,structural constituent of eye lens,2.08E-02
greenyellow,CC,1.96E-04,3.72,4.15,13,806,cytoskeletal part,2.59E-02
greenyellow,BP,3.20E-04,26.20,0.14,3,26,phototransduction,3.40E-01
grey60,BP,5.86E-04,21.35,0.17,3,86,respiratory electron transport chain,3.45E-01
grey60,CC,9.20E-04,18.08,0.19,3,105,mitochondrial membrane part,9.38E-02
lightcyan,MF,1.33E-05,87.57,0.05,3,47,"ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism",9.86E-04
lightcyan,MF,2.65E-05,68.73,0.06,3,59,"ATPase activity, coupled to transmembrane movement of ions",1.96E-03
lightcyan,BP,4.23E-05,56.87,0.07,3,57,ATP biosynthetic process,7.14E-03
lightcyan,BP,6.57E-05,48.71,0.08,3,66,purine ribonucleoside triphosphate biosynthetic process,1.11E-02
lightcyan,BP,6.87E-05,47.94,0.08,3,67,purine nucleoside triphosphate biosynthetic process,1.16E-02
lightcyan,BP,6.87E-05,47.94,0.08,3,67,ribonucleoside triphosphate biosynthetic process,1.16E-02
lightcyan,BP,7.50E-05,46.48,0.09,3,69,nucleoside triphosphate biosynthetic process,1.27E-02
lightcyan,MF,9.10E-05,44.64,0.09,3,89,"ATPase activity, coupled to transmembrane movement of substances",6.74E-03
lightcyan,MF,9.41E-05,44.12,0.09,3,90,"hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances",6.96E-03
lightcyan,MF,9.41E-05,44.12,0.09,3,90,"ATPase activity, coupled to movement of substances",6.96E-03
lightgreen,MF,7.38E-07,13.39,1.65,10,1128,receptor activity,6.64E-05
lightgreen,BP,1.56E-06,61.86,0.09,4,56,antigen processing and presentation,8.78E-04
lightgreen,MF,7.00E-06,10.17,2.10,10,1438,signal transducer activity,6.30E-04
lightgreen,MF,7.00E-06,10.17,2.10,10,1438,molecular transducer activity,6.30E-04
lightgreen,CC,1.20E-05,7.40,5.32,15,3146,plasma membrane,1.03E-03
lightgreen,BP,1.43E-05,706.81,0.01,2,4,cobalamin metabolic process,8.05E-03
lightgreen,BP,1.43E-05,706.81,0.01,2,4,cobalamin transport,8.05E-03
lightgreen,CC,1.47E-05,7.25,5.40,15,3195,cell periphery,1.26E-03
lightgreen,BP,2.38E-05,471.17,0.01,2,5,cobalt ion transport,1.34E-02
lightgreen,MF,4.22E-05,309.15,0.01,2,7,cobalamin binding,3.79E-03
magenta,CC,3.29E-04,3.39,31.31,43,7625,intracellular organelle,4.40E-02
magenta,CC,3.51E-04,3.37,31.38,43,7641,organelle,4.70E-02
magenta,CC,4.21E-04,4.53,36.84,47,8972,intracellular part,5.65E-02
magenta,BP,5.26E-04,78.28,0.04,2,8,regulation of centrosome cycle,3.31E-01
magenta,CC,5.77E-04,2.91,28.36,40,6906,intracellular membrane-bounded organelle,7.74E-02
magenta,CC,6.01E-04,2.90,28.40,40,6916,membrane-bounded organelle,8.05E-02
magenta,CC,8.90E-04,4.21,37.59,47,9154,intracellular,1.19E-01
pink,CC,2.43E-13,8.95,3.97,24,704,extracellular space,2.92E-11
pink,CC,3.65E-12,6.04,9.14,33,1621,extracellular region,4.38E-10
pink,MF,3.94E-12,16.53,1.12,14,186,cytokine activity,1.10E-09
pink,CC,5.52E-12,7.34,5.04,25,894,extracellular region part,6.62E-10
pink,MF,8.92E-09,12.55,1.08,11,180,cytokine receptor binding,2.50E-06
pink,BP,4.49E-08,5.64,4.50,19,772,defense response,4.50E-05
pink,MF,2.27E-07,28.39,0.27,6,44,chemokine activity,6.36E-05
pink,MF,3.87E-07,25.68,0.29,6,48,chemokine receptor binding,1.08E-04
pink,BP,2.69E-06,3.95,7.05,21,1211,immune system process,2.70E-03
pink,BP,7.19E-06,4.40,4.54,16,780,immune response,7.20E-03
purple,CC,1.73E-26,62.69,0.56,20,111,intermediate filament,2.51E-24
purple,CC,1.54E-24,48.65,0.69,20,137,intermediate filament cytoskeleton,2.23E-22
purple,CC,2.31E-11,7.92,4.09,22,806,cytoskeletal part,3.35E-09
purple,CC,9.80E-10,5.96,5.99,24,1181,cytoskeleton,1.42E-07
purple,BP,1.61E-06,30.60,0.20,5,56,negative regulation of endopeptidase activity,9.00E-04
purple,MF,5.95E-06,22.94,0.26,5,71,serine-type endopeptidase inhibitor activity,1.22E-03
purple,BP,1.14E-05,19.96,0.30,5,83,negative regulation of peptidase activity,6.36E-03
purple,BP,4.09E-05,15.08,0.39,5,108,regulation of proteolysis,2.29E-02
purple,CC,4.55E-05,3.05,10.63,24,2096,non-membrane-bounded organelle,6.59E-03
purple,CC,4.55E-05,3.05,10.63,24,2096,intracellular non-membrane-bounded organelle,6.59E-03
red,CC,5.07E-05,2.64,57.10,75,7625,intracellular organelle,1.21E-02
red,CC,5.60E-05,2.62,57.22,75,7641,organelle,1.34E-02
red,CC,5.65E-05,3.21,67.19,83,8972,intracellular part,1.35E-02
red,CC,7.02E-05,2.26,33.53,52,4478,organelle part,1.68E-02
red,CC,1.09E-04,2.21,33.09,51,4419,intracellular organelle part,2.61E-02
red,MF,1.19E-04,2.32,47.35,65,6043,protein binding,4.06E-02
red,CC,1.58E-04,2.31,51.72,69,6906,intracellular membrane-bounded organelle,3.77E-02
red,CC,1.67E-04,2.30,51.79,69,6916,membrane-bounded organelle,4.00E-02
red,CC,1.81E-04,2.98,68.55,83,9154,intracellular,4.32E-02
red,BP,2.06E-04,32.26,0.12,3,15,embryonic hindlimb morphogenesis,2.76E-01
salmon,BP,2.42E-07,47.72,0.14,5,67,biomineral tissue development,5.98E-05
salmon,CC,7.41E-06,5.87,3.92,14,1621,extracellular region,6.97E-04
salmon,CC,1.18E-04,176.91,0.02,2,7,voltage-gated sodium channel complex,1.11E-02
salmon,MF,2.49E-04,111.34,0.02,2,10,voltage-gated sodium channel activity,3.26E-02
salmon,CC,2.51E-04,110.54,0.02,2,10,sodium channel complex,2.36E-02
salmon,BP,4.44E-04,78.97,0.03,2,15,defense response to fungus,1.10E-01
salmon,BP,8.81E-04,54.00,0.04,2,21,killing of cells of other organism,2.18E-01
tan,CC,1.61E-04,4.63,2.47,10,432,ribonucleoprotein complex,2.37E-02
tan,BP,1.70E-04,190.95,0.02,2,4,selenocysteine incorporation,1.23E-01
tan,BP,1.70E-04,190.95,0.02,2,4,translational readthrough,1.23E-01
tan,CC,5.21E-04,3.28,52.33,64,9154,intracellular,7.66E-02
tan,CC,5.41E-04,3.67,3.42,11,598,nucleoplasm part,7.96E-02
tan,BP,5.91E-04,2.42,16.69,29,3100,gene expression,4.29E-01
tan,BP,7.69E-04,2.36,26.23,39,4871,cellular macromolecule metabolic process,5.58E-01
turquoise,BP,4.21E-11,2.44,42.06,86,388,sensory perception,2.07E-07
turquoise,CC,3.42E-10,1.62,178.69,255,1621,extracellular region,1.99E-07
turquoise,BP,1.98E-09,3.02,20.16,49,186,visual perception,9.71E-06
turquoise,BP,1.98E-09,3.02,20.16,49,186,sensory perception of light stimulus,9.71E-06
turquoise,BP,7.90E-08,9.70,2.82,14,26,phototransduction,3.88E-04
turquoise,CC,2.57E-06,1.67,77.60,117,704,extracellular space,1.50E-03
turquoise,BP,3.22E-06,6.12,3.58,14,33,detection of light stimulus,1.58E-02
turquoise,BP,5.17E-06,1.31,452.55,524,4175,multicellular organismal process,2.54E-02
turquoise,CC,5.74E-06,28.39,0.99,7,9,photoreceptor inner segment,3.34E-03
turquoise,CC,6.24E-06,8.13,2.43,11,22,high-density lipoprotein particle,3.63E-03
yellow,CC,4.49E-05,1.70,140.34,171,6916,membrane-bounded organelle,1.44E-02
yellow,CC,6.96E-05,1.67,140.13,170,6906,intracellular membrane-bounded organelle,2.23E-02
yellow,CC,2.40E-04,1.58,86.02,113,4239,nucleus,7.68E-02
yellow,CC,3.10E-04,1.75,185.75,209,9154,intracellular,9.92E-02
yellow,MF,4.08E-04,Inf,0.04,2,2,glutamate dehydrogenase activity,2.25E-01
yellow,MF,4.08E-04,Inf,0.04,2,2,glutamate dehydrogenase [NAD(P)+] activity,2.25E-01
yellow,MF,4.08E-04,Inf,0.04,2,2,"oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor",2.25E-01
yellow,MF,4.08E-04,Inf,0.04,2,2,leucine binding,2.25E-01
yellow,CC,4.77E-04,1.69,182.06,205,8972,intracellular part,1.53E-01
yellow,CC,5.66E-04,1.58,155.05,180,7641,organelle,1.81E-01
{csv}

h3.  Network and network diagnostics based on M value data (normalization is similar to the one above but +center+ was retained)

The reason for going into trouble and doing another round of normalization without removing the center is Justin's comment who suggested that center may be associated with patients who come with different genetic backgrounds (different CNV profiles). If this is the case by removing the center we will get rid suck out the "genetic" component and this could be the reason why we don't see the characteristic clustering of CpGs within almost every module defined by the comethylation network. This was seen with the data for which only the methylated probes were used (see [here|METHYLATION:Analysis of chromosomal positions of CpGs within each module (CpGchromosome)])


h3.!CorHeatmap.jpg|thumbnail! !GeneDendrogram.jpg|thumbnail! !ScaleFree.jpg|thumbnail!

Beta is 7, R^2=0.89. Number of modules = 8 
|| Module || \#of loci ||
| black | 41 |
| blue | 938 |
| brown | 408 |
| green | 135 |
| pink | 34 |
| red | 45 |
| turquoise | 1750 |
| yellow | 159 |
Percent variance explained by the first PC of each module and variability of the first PC of each module: !PercentVarianceExplained_Eigen1.png|thumbnail!  !Eigen1_variablity.png|thumbnail!