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

Results: HTML CSV LaTeX

Showing element 8241 to 8290 of 16578 in total

Value Type  : Measured
Filtered  : 1

description	Rank	Interaction Map	Network Comparison Type	red	network_comparison	green
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	2979	Low confidence	Divided	7788.78	1.02813	8007.87
	3128		Subtracted		219.09
mg81 protein (fragment). [sptrembl;acc:q14830]	639			8154.34	355.42	8509.76
	683		Divided		1.04359
mhc class ii regulatory factor rfx1 (rfx) (enhancer factor c) (ef-c). [swissprot;acc:p22670]	3024			7831.78	1.02795	8050.7
	3131		Subtracted		218.92
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	19	High confidence	Divided	677.5	2.75351	1865.5
	77	Low confidence		5334.13	1.11235	5933.4
	183		Subtracted		599.27
	281	High confidence		677.5	1188	1865.5
microfibrillar-associated protein 1. [swissprot;acc:p55081]	2949		Divided	0.00001	1	0.00001
			Subtracted	0	0	0
	4892	Low confidence		8430.75	60.73	8491.48
	4895		Divided		1.0072
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	230			7789.89	1.06529	8298.46
	249		Subtracted		508.57
	358	High confidence	Divided	5061.11	1.17567	5950.22
	450		Subtracted		889.11
microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005]	1290	Low confidence	Divided	7696.72	1.03542	7969.31
	1463		Subtracted		272.59
	2325	High confidence		5123.89	226.89	5350.78
	2335		Divided		1.04428
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	2424	Low confidence		7799.81	1.0306	8038.49
	2519		Subtracted		238.68
	2663	High confidence	Divided	4608.54	1.00703	4576.35
	2678		Subtracted		32.19
microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]	2643		Divided	5935.71	1.01012	5876.22
	2650		Subtracted		59.49
	2850	Low confidence	Divided	7766.61	1.02879	7990.22
	2994		Subtracted		223.61
microtubule-associated protein 7. [refseq;acc:nm_003980]	1450		Divided	7686.1	1.03432	7949.9
	1744		Subtracted		263.8
microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691]	1620	High confidence		6298.81	423.84	6722.65
	1744		Divided		1.06729
	2106	Low confidence	Subtracted	8078	252.46	8330.46
	2260		Divided		1.03125
microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8]	1618	High confidence	Subtracted	6298.77	423.85	6722.62
	1745		Divided		1.06729
	2098	Low confidence	Subtracted	8077.72	252.83	8330.55
	2249		Divided		1.0313
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	1617	High confidence	Subtracted	6298.76	423.85	6722.61
	1742		Divided		1.06729
	2095	Low confidence	Subtracted	8077.66	252.91	8330.57
	2245		Divided		1.03131
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	18	High confidence	Subtracted	24255.7	6086.8	18168.9
	28	Low confidence		13466.8	1814.4	11652.4
	50		Divided		1.15571
	125	High confidence		24255.7	1.33501	18168.9
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	17		Subtracted		6086.8
	27	Low confidence		13470.1	1815.7	11654.4

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.