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

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Showing element 1 to 16 of 16 in total

Rank  : 37
Network Comparison Type  : Divided

description	Filtered	network_comparison	Interaction Map	Value Type	green	red
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	0	2.79409	High confidence	Measured	934.348	334.401
		10.2338		Squared	1034.13	101.05
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	1	1.14874	Low confidence	Ranked	217.843	250.244
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	0	1.49458	High confidence		2582	3859
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	1	1.65293		Rooted	24.3691	40.2805
		2.02339		Measured	907.763	1836.76
jun dimerization protein. [refseq;acc:nm_130469]		1.17513	Low confidence		7593.77	6462.09
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	0	9.62112		Squared	0.355148	3.41692
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]		1.69589		Rooted	5.80678	9.84765
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]		2.97183		Measured	35.5	105.5
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	1	1.33073		Squared	61881.5	82347.8
myotubularin related protein 8. [refseq;acc:nm_017677]	0	1.36786		Ranked	8993.6	12302
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	1	1.80879	High confidence	Squared	192141	106226
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]		1.27273		Ranked	253	322
small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	0	1.94348		Rooted	9.39626	4.83477
testis-specific protein tex28. [swissprot;acc:o15482]	1	1.14428	Low confidence		59.166	51.7058

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.