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

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Showing element 2350 to 2399 of 66312 in total

Filtered  : 1

description	Rank	Value Type	green	Interaction Map	Network Comparison Type	network_comparison	red
60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	2115	Measured	3482.34	High confidence	Divided	1.0546	3672.49
	2397				Subtracted	190.15
	2444	Squared	13887.8			1221	12666.8
	2872		40882.9	Low confidence	Divided	1.03644	42372.8
	3165				Subtracted	1489.9
	4239	Measured	7712.96		Divided	1.01991	7562.4
	4459				Subtracted	150.56
	4670	Ranked	206.721			1.192	205.529
	4684				Divided	1.0058
	4711	Rooted	71.0591			1.01779	69.8173
	4749				Subtracted	1.2418
60s ribosomal protein l23a. [swissprot;acc:p29316]	243	Ranked	265.945	High confidence		24.061	241.884
	323				Divided	1.09947
	424	Rooted	45.9373			1.09868	50.4703
	688				Subtracted	4.533
	1950	Squared	13806.3		Divided	1.09293	12632.4
	2175	Measured	3463.88			1.05146	3642.13
	2243	Squared	40010.9	Low confidence		1.03892	41568.2
	2421	Measured	3463.88	High confidence	Subtracted	178.25	3642.13
	2479	Squared	13806.3			1173.9	12632.4
	2912		40010.9	Low confidence		1557.3	41568.2
	4107	Ranked	209.511			2.16	207.351
	4167				Divided	1.01042
	4610	Measured	7557.49			1.01653	7434.61
	4665				Subtracted	122.88
	4840	Rooted	70.0169		Divided	1.01384	69.0608
	4855				Subtracted	0.9561
60s ribosomal protein l24 (l30). [swissprot;acc:p38663]	335	Squared	37652.3	High confidence		6728	30924.3
	420				Divided	1.21756
	510	Measured	7911.25		Subtracted	824.02	7087.23
	727				Divided	1.11627
	994	Rooted	73.3177		Subtracted	3.42	69.8977
	1128				Divided	1.04893
	1767	Ranked	198.86			1.01221	201.288
	1821				Subtracted	2.428
	2829	Measured	8102.83	Low confidence	Divided	1.02894	7874.91
	2833	Squared	43146.2		Subtracted	1573.3	44719.5
	2865				Divided	1.03646
	2876	Measured	8102.83		Subtracted	227.92	7874.91
	3323	Rooted	73.4382		Divided	1.03093	71.2349
	3393				Subtracted	2.2033
	3900	Ranked	200.897			2.517	203.414
	3921				Divided	1.01253
60s ribosomal protein l26. [swissprot;acc:q02877]	217		267.008	High confidence	Subtracted	24.682	242.326
	302				Divided	1.10185
	374	Rooted	45.5599			1.10305	50.2549
	639				Subtracted	4.695
	1997	Squared	13513		Divided	1.09151	12380.1
	2051	Measured	3409.48			1.05646	3601.97
	2388				Subtracted	192.49

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.