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

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Showing element 97 to 146 of 66312 in total

Filtered  : 1

description	Rank	Network Comparison Type	Value Type	Hugo	Interaction Map	red	green	network_comparison
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (ec 3.1.4.11) (phosphoinositide phospholipase c) (plc-beta-4) (phospholipase c-beta-4). [swissprot;acc:q15147]	3126	Subtracted	Measured	PLCB4	High confidence	0	0	0
			Ranked
			Squared
			Rooted
	3189	Divided			Low confidence	71.5946	73.847	1.03146
	3244	Subtracted						2.2524
	3567		Ranked			202.517	199.628	2.889
	3585	Divided						1.01447
10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984]	588		Squared	HSPE1	High confidence	23526.4	27879.3	1.18502
	688	Subtracted						4352.9
	1136	Divided	Measured			5790.65	6303.92	1.08864
	1140	Subtracted						513.27
	1902		Rooted			63.4353	65.2789	1.8436
	1907	Divided						1.02906
	1933	Subtracted	Ranked			211.633	213.703	2.07
	1963	Divided						1.00978
	2020	Subtracted	Measured		Low confidence	8130.62	8386.58	255.96
	2182	Divided						1.03148
	2376	Subtracted	Rooted			72.718	75.1674	2.4494
	2477	Divided						1.03368
	2659		Ranked			200.053	196.574	1.0177
	2668	Subtracted						3.479
	3743		Squared			46195.2	44870.2	1325
	3878	Divided						1.02953
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891]	1632		Rooted	ALDH1L1		71.5773	74.1551	1.03601
	1693		Measured			7981.12	8246.34	1.03323
	1700	Subtracted						265.22
	1730		Rooted			71.5773	74.1551	2.5778
	1795		Ranked			203.414	199.455	3.959
	1873	Divided						1.01985
	2922		Measured		High confidence	0.00001	0.00001	1
			Ranked
			Squared
			Rooted
		Subtracted	Measured			0	0	0
			Ranked
			Squared
			Rooted
	3891		Squared		Low confidence	45711.3	44461.5	1249.8
	4003	Divided						1.02811
130 kda leucine-rich protein (lrp 130) (gp130) (leucine-rich ppr-motif containing protein). [swissprot;acc:p42704]	1727			LRPPRC		43932.5	42157.3	1.04211
	1957	Subtracted						1775.2
	4071	Divided	Measured			7896.47	8067.47	1.02166
	4138		Rooted			71.6344	73.4871	1.02586
	4228	Subtracted	Measured			7896.47	8067.47	171
	4255	Divided	Ranked			202.306	200.395	1.00954
	4263	Subtracted						1.911
	4303		Rooted			71.6344	73.4871	1.8527
14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946]	490		Measured	YWHAB		8572.9	8965.49	392.59
	575	Divided						1.04579

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
- Hugo is the HGNC identifier if it exists
- 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.