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	Network Comparison Type	Filtered	Interaction Map	red	network_comparison	green

Results: HTML CSV LaTeX

Showing element 2680 to 2729 of 7460 in total

Value Type  : Measured
Interaction Map  : High confidence

description	Rank	Network Comparison Type	Filtered	red	network_comparison	green
glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311]	2920	Subtracted	1	0	0	0
glycine receptor beta chain precursor (glycine receptor 58 kda subunit). [swissprot;acc:p48167]	3083	Divided		0.00001	1	0.00001
		Subtracted		0	0	0
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	61	Divided		4489.19	1.6231	2765.82
	165	Subtracted			1723.37
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	62	Divided			1.6231
	166	Subtracted			1723.37
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	64	Divided			1.6231
	168	Subtracted			1723.37
glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840]	1089			6439.79	519.42	6959.21
	1323	Divided			1.08066
glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841]	1090	Subtracted			519.42
	1324	Divided			1.08066
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840]	254	Subtracted		9634.98	1341.22	10976.2
	522	Divided			1.1392
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807]	252	Subtracted		9648.27	1346.63	10994.9
	519	Divided			1.13957
glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976]	1371	Subtracted		6376.12	457.47	6833.59
	1580	Divided			1.07175
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	74	Subtracted	0	14267.5	421.3	14688.8
	428	Divided			1.02953
	1374	Subtracted	1	6376.12	457.47	6833.59
	1583	Divided			1.07175
glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250]	1307			5500.92	1.0815	5949.26
	1434	Subtracted			448.34
gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915]	2208			5776.96	272.65	6049.61
	2244	Divided			1.0472
golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735]	697	Subtracted		5768.32	666.46	6434.78
	737	Divided			1.11554
golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799]	1133			5790.65	1.08864	6303.92
	1138	Subtracted			513.27
golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530]	325			8362.81	1039.89	9402.7
	650	Divided			1.12435
goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4]	501	Subtracted		10725.6	829.28	9896.32
	1254	Divided			1.0838
gpi transamidase component pig-s (phosphatidylinositol-glycan biosynthesis, class s protein). [swissprot;acc:q96s52]	3165			0.00001	1	0.00001
		Subtracted		0	0	0
grancalcin. [swissprot;acc:p28676]	393			6251.96	940.17	7192.13
	441	Divided			1.15038
grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791]	225	Subtracted		6417.19	1442.32	7859.51
	256	Divided			1.22476
grb2-related adaptor protein. [swissprot;acc:q13588]	458	Subtracted		5986.65	879.03	6865.68
	461	Divided			1.14683
growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522]	2493			3436.65	1.02773	3531.96
	2585	Subtracted			95.31
growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293]	2495	Divided			1.02773
	2587	Subtracted			95.31
growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257]	2492	Divided			1.02773
	2584	Subtracted			95.31
growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354]	486			5975.11	851.13	6826.24

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.