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	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 4080 to 4129 of 7460 in total

Value Type  : Ranked
Interaction Map  : High confidence

description	Rank	Network Comparison Type	Filtered	red	green	network_comparison
muts protein homolog 4. [swissprot;acc:o15457]	3194	Subtracted	1	0	0	0
muts protein homolog 5. [swissprot;acc:o43196]	3148	Divided		0.00001	0.00001	1
		Subtracted		0	0	0
my016 protein. [sptrembl;acc:q9h3k6]	166	Divided	0	5561.19	6366.91	1.14488
	288	Subtracted				805.72
	1387		1	224.755	229.2	4.445
	1451	Divided				1.01978
myb proto-oncogene protein (c-myb). [swissprot;acc:p10242]	1529	Subtracted		222.672	218.92	3.752
	1541	Divided				1.01714
myb-related protein a (a-myb). [swissprot;acc:p10243]	1539	Subtracted		222.512	218.802	3.71
	1548	Divided				1.01696
myb-related protein b (b-myb). [swissprot;acc:p10244]	1538	Subtracted		222.541	218.823	3.718
	1547	Divided				1.01699
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106]	856	Subtracted		227.585	219.037	8.548
	893	Divided				1.03903
myelin gene expression factor 2. [refseq;acc:nm_016132]	278	Subtracted		235.383	258.476	23.093
	340	Divided				1.09811
myelin p2 protein. [swissprot;acc:p02689]	2174	Subtracted		221.509	220.108	1.401
	2218	Divided				1.00637
myeloblast kiaa0230 (fragment). [sptrembl;acc:q92626]	3000			0.00001	0.00001	1
		Subtracted		0	0	0
myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368]	2290	Divided		200.158	201.213	1.00527
	2302	Subtracted				1.055
myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572]	1643	Divided		194.476	197.305	1.01455
	1715	Subtracted				2.829
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	215	Divided		112	126	1.125
	332		0	8125.5	7697.5	1.0556
	373	Subtracted				428
	532		1	112	126	14
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	221	Divided				1.125
	543	Subtracted				14
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	219	Divided				1.125
	541	Subtracted				14
myosin heavy chain, nonmuscle type a (cellular myosin heavy chain, type a) (nonmuscle myosin heavy chain-a) (nmmhc-a). [swissprot;acc:p35579]	3140	Divided		0.00001	0.00001	1
		Subtracted		0	0	0
myosin heavy chain, nonmuscle type b (cellular myosin heavy chain, type b) (nonmuscle myosin heavy chain-b) (nmmhc-b). [swissprot;acc:p35580]	2988	Divided		0.00001	0.00001	1
		Subtracted		0	0	0
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	220	Divided		112	126	1.125
	335		0	8125.5	7697.5	1.0556
	376	Subtracted				428
	542		1	112	126	14
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	218	Divided				1.125
	334		0	8125.5	7697.5	1.0556
	375	Subtracted				428
	539		1	112	126	14
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	223	Divided				1.125
	336		0	8125.5	7697.5	1.0556
	377	Subtracted				428
	546		1	112	126	14
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	216	Divided				1.125

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.