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

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Showing element 3632 to 3681 of 19268 in total

Value Type  : Ranked

description	Rank	Filtered	Network Comparison Type	Interaction Map	red	green	network_comparison
conserved oligomeric golgi complex component 1. [swissprot;acc:q8wtw3]	2836	1	Subtracted	High confidence	0	0	0
	4125		Divided	Low confidence	197.858	195.778	1.01062
	4181		Subtracted				2.08
conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746]	1176			High confidence	214.364	219.759	5.395
	1213		Divided				1.02517
	3817		Subtracted	Low confidence	202.207	199.576	2.631
	3827		Divided				1.01318
conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2]	346		Subtracted		206.433	198.781	7.652
	354		Divided				1.03849
	2604		Subtracted	High confidence	224.891	225.195	0.304
	2627		Divided				1.00135
conserved oligomeric golgi complex component 4. [swissprot;acc:q9h9e3]	3425			Low confidence	199.066	196.08	1.01523
	3450		Subtracted				2.986
conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7]	2110		Divided	High confidence	211.099	209.607	1.00712
	2131		Subtracted				1.492
	2939			Low confidence	200.603	197.255	3.348
	2941		Divided				1.01697
conserved oligomeric golgi complex component 7. [swissprot;acc:p83436]	2750			High confidence	190.522	190.496	1.00014
			Subtracted				0.026
	3844			Low confidence	200.983	198.394	2.589
	3848		Divided				1.01305
conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83]	186		Subtracted		215.723	205.046	10.677
	194		Divided				1.05207
	479		Subtracted	High confidence	220.172	235.98	15.808
	493		Divided				1.0718
contactin 2 precursor (axonin-1) (axonal glycoprotein tag-1) (transient axonal glycoprotein 1) (tax-1). [swissprot;acc:q02246]	4778			Low confidence	201.633	200.734	1.00448
	4779		Subtracted				0.899
contactin 5 isoform long; neural adhesion molecule. [refseq;acc:nm_014361]			Divided				1.00448
	4780		Subtracted				0.899
contactin 6; neural adhesion molecule. [refseq;acc:nm_014461]			Divided				1.00448
	4781		Subtracted				0.899
contactin associated protein 1 precursor (caspr) (caspr1) (neurexin 4) (neurexin iv) (p190). [swissprot;acc:p78357]	1822				208.784	204.84	3.944
	2098		Divided				1.01925
contactin associated protein-like 3 precursor (cell recognition molecule caspr3). [swissprot;acc:q9bz76]	623	0			1256	1294	1.03025
	812		Subtracted				38
	1824	1			208.784	204.84	3.944
	2100		Divided				1.01925
contactin associated protein-like 4 precursor (cell recognition molecule caspr4). [swissprot;acc:q9c0a0]	1821		Subtracted				3.944
	2097		Divided				1.01925
contactin precursor (glycoprotein gp135). [swissprot;acc:q12860]	4783				201.633	200.734	1.00448
	4784		Subtracted				0.899
cop-coated vesicle membrane protein p24 precursor (p24a). [swissprot;acc:q15363]	2564		Divided		191.257	187.872	1.01802
	2884		Subtracted				3.385
	3168		Divided	High confidence	0.00001	0.00001	1
			Subtracted		0	0	0
cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129]	1500		Divided		213.398	209.52	1.01851
	1501		Subtracted				3.878
	4804		Divided	Low confidence	202.289	201.442	1.0042
			Subtracted				0.847
cop9 complex subunit 7a; cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 7a. [refseq;acc:nm_016319]	3874				201.889	199.344	2.545

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.