Network and network diagnostics with M value based data (center, batch, plate row and column variables removed)
Check if the network is scale free. To do that I need to plot clustering coefficient against network connectivity. To calculate clustering coefficient:
- Use Bioconductor "graph" library
- Calculate positive adjacency matrix
adjM<-abs(cor(t(data)))
- Since taking a chunk of the adjacency matrix will give a good idea about the clustering coefficient and will significantly speed up the calculations Chris suggested to take 4k by 4k matrix and use hard thresholding. I used first 4k columns and rows.
Take a look at the distribution of the small adjacency matrix:
From the conversation with Chris it seems that I have very very few strong correlations and most of them are not that strong. Therefore when we are trying to use a scale free network (raising each correlation to the power of beta) it creates even smaller values and it impedes clustering into modules.
Hard threshold was 0.46 on the 4k by 4 k matrix to get about 1% of the nodes (adjM4000)
- To use it with the graph library change diagonal of the matrix to 0 (no self looping nodes!)
- Create an instance of the class graph and calculate clustering coefficient:
g4000<-new("graphAM",adjMat=adjMat4000) cc4000<-clusteringCoefficient(g4000)
To calculate connectivity get a sum of all columns of the hard-thresholded matrix (adjM4000):
kk<-apply(adjMat4000,2, sum)
Finally, get rid of all values in cc4000 and kk that are equal to 0 (which I didn't for this plot) and make a scatter plot:
If I do averaging of cc over k I can get an approximate straight line which is the evidence of the scale-free network (Barabasi, 2004). However, this plot is only a part of an the evaluation. I actually need to plot P(k) vs k to get a definite answer.
Another thing that was interesting to check is the variance of CpG loci vs connectivity. Apparently, in gene expression there is a linear relationship between these properties: more variable genes tend to be more connected. Tkae the same matrix of 4k by 4k, get var() value for each CpG and plot it. Also, plot mean value of each CpG across all patients in relation to the connectivity:
It is interesting to see that with DNA methylation the most connected genes are actually the least variable across patients. Does it really make biological sense? Do we expect this with this type of data? Could it be a reflection of the technology rather than biology (DNA methylation in itself is not a continuous trait although it might become on if we have many cells and a heterogeneous population of them). What if we take the most variable CpGs and build network out of them rather than all 27k?
Cytoscape view of the 4k network. Color: CpG variance (darker =more variable), size = number of connections
WGCNA
R version 2.13.0 64 bit, SageBionetworksCoex 0.11, running time ~4.5 hours (~27k by 486)
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:
With M value almost no modules were composed of the CpGs from a single chromosome (chromosomal density plots can be found here)
Modules lightcyan, lightgreen, salmon and yellow, >55% of the loci came from the same chromosome (plots are here)
Gene Ontology analyses of each module (top 10 categories were selected and KEGG pathways didn't work for my on that day):
Unknown macro: {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
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
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)
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:
Unknown macro: {csv} black,BP,1.13E-06,219.95,0.02,3,10,low-density lipoprotein particle remodeling,7.65E-04
black,BP,1.42E-05,80.95,0.05,3,22,macromolecular complex remodeling,9.64E-03
black,BP,1.42E-05,80.95,0.05,3,22,protein-lipid complex remodeling,9.64E-03
black,BP,1.42E-05,80.95,0.05,3,22,plasma lipoprotein particle remodeling,9.64E-03
black,MF,1.59E-05,13.64,0.56,6,233,enzyme inhibitor activity,3.03E-03
black,BP,2.27E-05,7.78,1.70,9,771,defense response,1.54E-02
black,BP,2.69E-05,64.06,0.06,3,27,protein-lipid complex subunit organization,1.82E-02
black,BP,2.69E-05,64.06,0.06,3,27,plasma lipoprotein particle organization,1.82E-02
black,MF,2.15E-04,15.79,0.30,4,125,peptidase inhibitor activity,4.08E-02
black,MF,3.04E-04,98.92,0.03,2,11,cGMP binding,5.78E-02
blue,CC,5.24E-11,1.89,101.38,164,1853,plasma membrane part,2.29E-08
blue,CC,2.92E-08,1.60,171.90,234,3142,plasma membrane,1.27E-05
blue,CC,4.58E-08,1.58,174.58,236,3191,cell periphery,2.00E-05
blue,BP,3.38E-07,2.06,37.90,70,707,cell adhesion,1.25E-03
blue,BP,3.38E-07,2.06,37.90,70,707,biological adhesion,1.25E-03
blue,CC,3.59E-07,1.83,60.18,99,1100,intrinsic to plasma membrane,1.57E-04
blue,MF,5.72E-07,1.82,60.14,98,1128,receptor activity,5.21E-04
blue,CC,7.91E-07,1.47,307.80,369,5626,membrane,3.45E-04
blue,BP,9.01E-07,6.68,2.57,13,48,cellular defense response,3.33E-03
blue,MF,1.13E-06,1.71,76.61,117,1437,signal transducer activity,1.03E-03
brown,CC,1.63E-05,1.82,125.31,156,6912,membrane-bounded organelle,5.20E-03
brown,CC,2.70E-05,1.79,125.13,155,6902,intracellular membrane-bounded organelle,8.61E-03
brown,CC,1.15E-04,1.73,138.45,165,7637,organelle,3.65E-02
brown,CC,1.73E-04,1.70,138.16,164,7621,intracellular organelle,5.52E-02
brown,CC,2.95E-04,1.61,76.83,102,4238,nucleus,9.42E-02
brown,MF,3.29E-04,Inf,0.04,2,2,glutamate dehydrogenase activity,1.75E-01
brown,MF,3.29E-04,Inf,0.04,2,2,glutamate dehydrogenase [NAD(P)+] activity,1.75E-01
brown,MF,3.29E-04,Inf,0.04,2,2,"oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor",1.75E-01
brown,MF,3.29E-04,Inf,0.04,2,2,leucine binding,1.75E-01
brown,CC,5.02E-04,1.77,165.83,187,9147,intracellular,1.60E-01
green,BP,1.48E-49,750.20,0.18,24,34,keratinization,9.94E-47
green,BP,8.62E-42,186.38,0.36,25,68,keratinocyte differentiation,5.80E-39
green,BP,1.65E-39,142.95,0.43,25,81,epidermal cell differentiation,1.11E-36
green,BP,2.98E-29,47.75,1.01,25,191,epithelial cell differentiation,2.00E-26
green,BP,9.89E-29,45.26,1.06,25,200,epidermis development,6.66E-26
green,CC,1.35E-26,53.92,0.66,21,111,intermediate filament,1.29E-24
green,CC,1.51E-24,41.74,0.82,21,137,intermediate filament cytoskeleton,1.44E-22
green,BP,3.20E-22,23.23,1.91,25,361,epithelium development,2.15E-19
green,BP,5.51E-14,9.68,4.23,25,799,tissue development,3.71E-11
green,CC,1.20E-12,6.63,7.04,30,1181,cytoskeleton,1.14E-10
grey,CC,4.47E-11,1.56,6375.91,6472,6902,intracellular membrane-bounded organelle,5.15E-08
grey,CC,4.95E-11,1.55,6385.15,6481,6912,membrane-bounded organelle,5.71E-08
grey,BP,2.83E-07,3.02,532.82,561,577,embryo development,2.64E-03
grey,BP,9.13E-07,1.44,3919.04,3984,4244,nitrogen compound metabolic process,8.50E-03
grey,BP,1.86E-06,1.39,6000.45,6066,6498,cellular metabolic process,1.73E-02
grey,BP,2.28E-06,1.42,3836.85,3899,4155,cellular nitrogen compound metabolic process,2.13E-02
grey,BP,3.75E-06,1.53,2159.90,2210,2339,RNA metabolic process,3.49E-02
grey,CC,4.17E-06,1.36,7054.89,7120,7637,organelle,4.80E-03
grey,CC,4.52E-06,1.36,7040.11,7105,7621,intracellular organelle,5.21E-03
grey,CC,6.34E-06,1.38,8281.66,8341,8965,intracellular part,7.30E-03
red,BP,6.30E-04,66.15,0.04,2,13,"regulation of transcription elongation, DNA-dependent",4.57E-01
turquoise,BP,6.44E-08,2.22,35.12,68,388,sensory perception,2.95E-04
turquoise,CC,1.97E-07,1.54,149.16,207,1621,extracellular region,1.09E-04
turquoise,BP,4.70E-07,2.73,16.84,39,186,visual perception,2.16E-03
turquoise,BP,4.70E-07,2.73,16.84,39,186,sensory perception of light stimulus,2.16E-03
turquoise,BP,8.27E-07,8.70,2.35,12,26,phototransduction,3.80E-03
turquoise,CC,9.64E-06,8.29,2.02,10,22,high-density lipoprotein particle,5.34E-03
turquoise,BP,1.13E-05,2.81,11.77,28,130,regulation of lipid metabolic process,5.16E-02
turquoise,BP,1.67E-05,5.80,2.99,12,33,detection of light stimulus,7.66E-02
turquoise,BP,2.21E-05,1.32,377.85,439,4174,multicellular organismal process,1.01E-01
turquoise,CC,2.79E-05,1.63,64.78,97,704,extracellular space,1.55E-02
yellow,CC,4.35E-07,2.40,47.69,76,4417,intracellular organelle part,1.16E-04
yellow,CC,7.93E-07,2.35,48.33,76,4476,organelle part,2.11E-04
yellow,CC,4.62E-06,2.90,11.85,29,1098,nucleoplasm,1.23E-03
yellow,CC,6.25E-06,2.50,19.11,39,1770,nuclear part,1.66E-03
yellow,CC,8.23E-06,2.44,20.08,40,1860,intracellular organelle lumen,2.19E-03
yellow,CC,8.70E-06,2.28,74.52,99,6902,intracellular membrane-bounded organelle,2.31E-03
yellow,CC,9.45E-06,2.27,74.63,99,6912,membrane-bounded organelle,2.51E-03
yellow,CC,1.42E-05,2.38,20.54,40,1902,organelle lumen,3.77E-03
yellow,CC,1.95E-05,2.29,82.28,105,7621,intracellular organelle,5.18E-03
yellow,CC,2.11E-05,2.33,20.88,40,1934,membrane-enclosed lumen,5.62E-03
black,BP,1.42E-05,80.95,0.05,3,22,macromolecular complex remodeling,9.64E-03
black,BP,1.42E-05,80.95,0.05,3,22,protein-lipid complex remodeling,9.64E-03
black,BP,1.42E-05,80.95,0.05,3,22,plasma lipoprotein particle remodeling,9.64E-03
black,MF,1.59E-05,13.64,0.56,6,233,enzyme inhibitor activity,3.03E-03
black,BP,2.27E-05,7.78,1.70,9,771,defense response,1.54E-02
black,BP,2.69E-05,64.06,0.06,3,27,protein-lipid complex subunit organization,1.82E-02
black,BP,2.69E-05,64.06,0.06,3,27,plasma lipoprotein particle organization,1.82E-02
black,MF,2.15E-04,15.79,0.30,4,125,peptidase inhibitor activity,4.08E-02
black,MF,3.04E-04,98.92,0.03,2,11,cGMP binding,5.78E-02
blue,CC,5.24E-11,1.89,101.38,164,1853,plasma membrane part,2.29E-08
blue,CC,2.92E-08,1.60,171.90,234,3142,plasma membrane,1.27E-05
blue,CC,4.58E-08,1.58,174.58,236,3191,cell periphery,2.00E-05
blue,BP,3.38E-07,2.06,37.90,70,707,cell adhesion,1.25E-03
blue,BP,3.38E-07,2.06,37.90,70,707,biological adhesion,1.25E-03
blue,CC,3.59E-07,1.83,60.18,99,1100,intrinsic to plasma membrane,1.57E-04
blue,MF,5.72E-07,1.82,60.14,98,1128,receptor activity,5.21E-04
blue,CC,7.91E-07,1.47,307.80,369,5626,membrane,3.45E-04
blue,BP,9.01E-07,6.68,2.57,13,48,cellular defense response,3.33E-03
blue,MF,1.13E-06,1.71,76.61,117,1437,signal transducer activity,1.03E-03
brown,CC,1.63E-05,1.82,125.31,156,6912,membrane-bounded organelle,5.20E-03
brown,CC,2.70E-05,1.79,125.13,155,6902,intracellular membrane-bounded organelle,8.61E-03
brown,CC,1.15E-04,1.73,138.45,165,7637,organelle,3.65E-02
brown,CC,1.73E-04,1.70,138.16,164,7621,intracellular organelle,5.52E-02
brown,CC,2.95E-04,1.61,76.83,102,4238,nucleus,9.42E-02
brown,MF,3.29E-04,Inf,0.04,2,2,glutamate dehydrogenase activity,1.75E-01
brown,MF,3.29E-04,Inf,0.04,2,2,glutamate dehydrogenase [NAD(P)+] activity,1.75E-01
brown,MF,3.29E-04,Inf,0.04,2,2,"oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor",1.75E-01
brown,MF,3.29E-04,Inf,0.04,2,2,leucine binding,1.75E-01
brown,CC,5.02E-04,1.77,165.83,187,9147,intracellular,1.60E-01
green,BP,1.48E-49,750.20,0.18,24,34,keratinization,9.94E-47
green,BP,8.62E-42,186.38,0.36,25,68,keratinocyte differentiation,5.80E-39
green,BP,1.65E-39,142.95,0.43,25,81,epidermal cell differentiation,1.11E-36
green,BP,2.98E-29,47.75,1.01,25,191,epithelial cell differentiation,2.00E-26
green,BP,9.89E-29,45.26,1.06,25,200,epidermis development,6.66E-26
green,CC,1.35E-26,53.92,0.66,21,111,intermediate filament,1.29E-24
green,CC,1.51E-24,41.74,0.82,21,137,intermediate filament cytoskeleton,1.44E-22
green,BP,3.20E-22,23.23,1.91,25,361,epithelium development,2.15E-19
green,BP,5.51E-14,9.68,4.23,25,799,tissue development,3.71E-11
green,CC,1.20E-12,6.63,7.04,30,1181,cytoskeleton,1.14E-10
grey,CC,4.47E-11,1.56,6375.91,6472,6902,intracellular membrane-bounded organelle,5.15E-08
grey,CC,4.95E-11,1.55,6385.15,6481,6912,membrane-bounded organelle,5.71E-08
grey,BP,2.83E-07,3.02,532.82,561,577,embryo development,2.64E-03
grey,BP,9.13E-07,1.44,3919.04,3984,4244,nitrogen compound metabolic process,8.50E-03
grey,BP,1.86E-06,1.39,6000.45,6066,6498,cellular metabolic process,1.73E-02
grey,BP,2.28E-06,1.42,3836.85,3899,4155,cellular nitrogen compound metabolic process,2.13E-02
grey,BP,3.75E-06,1.53,2159.90,2210,2339,RNA metabolic process,3.49E-02
grey,CC,4.17E-06,1.36,7054.89,7120,7637,organelle,4.80E-03
grey,CC,4.52E-06,1.36,7040.11,7105,7621,intracellular organelle,5.21E-03
grey,CC,6.34E-06,1.38,8281.66,8341,8965,intracellular part,7.30E-03
red,BP,6.30E-04,66.15,0.04,2,13,"regulation of transcription elongation, DNA-dependent",4.57E-01
turquoise,BP,6.44E-08,2.22,35.12,68,388,sensory perception,2.95E-04
turquoise,CC,1.97E-07,1.54,149.16,207,1621,extracellular region,1.09E-04
turquoise,BP,4.70E-07,2.73,16.84,39,186,visual perception,2.16E-03
turquoise,BP,4.70E-07,2.73,16.84,39,186,sensory perception of light stimulus,2.16E-03
turquoise,BP,8.27E-07,8.70,2.35,12,26,phototransduction,3.80E-03
turquoise,CC,9.64E-06,8.29,2.02,10,22,high-density lipoprotein particle,5.34E-03
turquoise,BP,1.13E-05,2.81,11.77,28,130,regulation of lipid metabolic process,5.16E-02
turquoise,BP,1.67E-05,5.80,2.99,12,33,detection of light stimulus,7.66E-02
turquoise,BP,2.21E-05,1.32,377.85,439,4174,multicellular organismal process,1.01E-01
turquoise,CC,2.79E-05,1.63,64.78,97,704,extracellular space,1.55E-02
yellow,CC,4.35E-07,2.40,47.69,76,4417,intracellular organelle part,1.16E-04
yellow,CC,7.93E-07,2.35,48.33,76,4476,organelle part,2.11E-04
yellow,CC,4.62E-06,2.90,11.85,29,1098,nucleoplasm,1.23E-03
yellow,CC,6.25E-06,2.50,19.11,39,1770,nuclear part,1.66E-03
yellow,CC,8.23E-06,2.44,20.08,40,1860,intracellular organelle lumen,2.19E-03
yellow,CC,8.70E-06,2.28,74.52,99,6902,intracellular membrane-bounded organelle,2.31E-03
yellow,CC,9.45E-06,2.27,74.63,99,6912,membrane-bounded organelle,2.51E-03
yellow,CC,1.42E-05,2.38,20.54,40,1902,organelle lumen,3.77E-03
yellow,CC,1.95E-05,2.29,82.28,105,7621,intracellular organelle,5.18E-03
yellow,CC,2.11E-05,2.33,20.88,40,1934,membrane-enclosed lumen,5.62E-03
I think it is interesting that in both networks a module has been identified that is highly enriched in categories such as keratinization, epidermal cell differentiation, epithelial cells differentiation, epidermis development etc (module "green" in both cases).