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

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Showing element 1 to 50 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

description	Value Type	Rank	red	green	network_comparison	Filtered
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Measured	37	334.401	934.348	2.79409	0
		60	4489.19	2765.82	1.6231	1
	Ranked	18	185.678	245.247	1.32082
		242	15260.6	13895.8	1.09822	0
	Squared	37	101.05	1034.13	10.2338
		245	8875.01	6768.05	1.31131	1
	Rooted	53	11.844	18.0183	1.5213	0
		64	63.8686	47.2654	1.35128	1
1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943]	Measured	509	7551.8	8630.06	1.14278
	Ranked	1038	186.741	181.041	1.03148
	Squared	295	30807.7	39351.7	1.27733
	Rooted	805	74.3557	79.1513	1.0645
1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120]	Measured	508	7556.75	8636.87	1.14293
	Ranked	1032	186.664	180.943	1.03162
	Squared	294	30826.5	39383.9	1.2776
	Rooted	804	74.3877	79.1931	1.0646
1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5]	Measured	514	7477	8532.02	1.1411
	Ranked	1048	187.96	182.308	1.031
	Squared	311	30566.4	38866.5	1.27154
	Rooted	822	73.8577	78.5795	1.06393
1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7]	Measured	513	7485.08	8543.66	1.14143
	Ranked	1043	187.834	182.137	1.03128
	Squared	308	30596.2	38919.9	1.27205
	Rooted	811	73.9102	78.6514	1.06415
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]	Measured	3126	0.00001	0.00001	1
	Ranked
	Squared
	Rooted
10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984]	Measured	1136	5790.65	6303.92	1.08864
	Ranked	1963	211.633	213.703	1.00978
	Squared	588	23526.4	27879.3	1.18502
	Rooted	1907	63.4353	65.2789	1.02906
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891]	Measured	2922	0.00001	0.00001	1
	Ranked
	Squared
	Rooted
14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946]	Measured	1411	5812.02	6262.07	1.07743
	Ranked	2439	220.681	221.425	1.00337
	Squared	1143	28551.5	32561.8	1.14046
	Rooted	1943	61.3337	63.0838	1.02853
14-3-3 protein epsilon (mitochondrial import stimulation factor l subunit) (protein kinase c inhibitor protein-1) (kcip-1) (14-3-3e). [swissprot;acc:p42655]	Measured	3088	0.00001	0.00001	1
	Ranked
	Squared
	Rooted
14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312]	Measured	1415	5815.33	6265.44	1.0774
	Ranked	2396	220.683	221.51	1.00375
	Squared	1135	28600.9	32641.7	1.14128
	Rooted	1961	61.3419	63.0743	1.02824
14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758]	Measured	1600	6336.22	6788.96	1.07145
	Ranked	2366	203.353	202.529	1.00407

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.