MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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network_comparison	green	Filtered	description	Interaction Map	Value Type	Network Comparison Type	Rank	red	Gene

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Showing element 1101 to 1150 of 38536 in total

network_comparison  : 1
green  : 0.00001
Filtered  : 1
Interaction Map  : High confidence
Network Comparison Type  : Divided
red  : 0.00001

description	Value Type	Rank
nov protein homolog precursor (novh) (nephroblastoma overexpressed gene protein homolog). [swissprot;acc:p48745]	Measured	2970
	Ranked
	Squared
	Rooted
nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]	Measured	3184
	Ranked
	Squared
	Rooted
nuclear factor related to kappa b binding protein. [refseq;acc:nm_006165]	Measured	2823
	Ranked
	Squared
	Rooted
nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [swissprot;acc:p35658]	Measured	3008
	Ranked
	Squared
	Rooted
nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [swissprot;acc:p13662]	Measured	3113
	Ranked
	Squared
	Rooted
nucleolar phosphoprotein p130 (nucleolar 130 kda protein) (140 kda nucleolar phosphoprotein) (nopp140) (nucleolar and coiled-body phosphoprotein 1). [swissprot;acc:q14978]	Measured	2842
	Ranked
	Squared
	Rooted
nucleophosmin (npm) (nucleolar phosphoprotein b23) (numatrin) (nucleolar protein no38). [swissprot;acc:p06748]	Measured	2785
	Ranked
	Squared
	Rooted
nucleoplasmin 3. [swissprot;acc:o75607]	Measured	3096
	Ranked
	Squared
	Rooted
nucleoporin 50 kda (nuclear pore-associated protein 60 kda-like) (pro1146). [swissprot;acc:q9ukx7]	Measured	3154
	Ranked
	Squared
	Rooted
nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209]	Measured	2757
	Ranked
	Squared
	Rooted
nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [swissprot;acc:q9ulw6]	Measured	2758
	Ranked
	Squared
	Rooted
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	Measured	3080
	Ranked
	Squared
	Rooted
origin recognition complex subunit 2. [swissprot;acc:q13416]	Measured	3047
	Ranked

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.