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

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Showing element 551 to 600 of 38536 in total

Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided

description	green	Interaction Map	network_comparison	Rank	red
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	High confidence	8900000	4	0.00001
		Low confidence		2
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		High confidence		5
		Low confidence		3
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	4459.15		1.00194	819	4467.8
	6254.09	High confidence	1.01102	465	6323
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0.00001		1	499	0.00001
		Low confidence	1300000	6	13
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	650.724	High confidence	1.15407	223	750.981
	767.529	Low confidence	1.08926	423	704.635
huntingtin interacting protein c. [refseq;acc:nm_012272]	1296.38	High confidence	1.27566	160	1653.74
	2896.88	Low confidence	1.05011	565	2758.64
huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	39485	High confidence	1.00817	470	39165
		Low confidence		782
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	327.517	High confidence	1.92644	55	630.942
	2877.82	Low confidence	1.05288	549	2733.29
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	5.71669	High confidence	34.8539	12	199.249
		Low confidence		11
hyaluronan and proteoglycan link protein 3. [refseq;acc:nm_178232]	1162.04		1.11685	374	1297.83
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597]	2059.13		1.0612	492	1940.37
	2220.68	High confidence	1.06988	344	2075.64
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	8713.64	Low confidence	1.0489	568	8307.37
	12011.7	High confidence	1.04338	389	11512.3
importin 4. [refseq;acc:nm_024658]	476.639		1.03207	421	491.926
	3599.83	Low confidence	1.02232	675	3521.22
importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	115.333	High confidence	1.65896	82	191.333
	1926.2	Low confidence	1.05454	539	1826.57
importin 9. [refseq;acc:nm_018085]	1397.66	High confidence	1.22221	187	1143.55
	1658.37	Low confidence	1.01261	748	1679.28
importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	1068	High confidence	1.75947	70	607
	2827.2	Low confidence	1.01529	719	2784.62
inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	416.524	High confidence	1.70956	77	712.071
	2268.54	Low confidence	1.01904	691	2311.73
inositol polyphosphate-5-phosphatase, 145kda; hp51cn; inositol polyphosphate-5-phosphatase, 145kd. [refseq;acc:nm_005541]	1245.48		1.05472	537	1180.86
integral membrane protein cii-3b. [sptrembl;acc:o75609]	2091.88		1.10051	407	2302.14
	2304.22	High confidence	1.03858	405	2218.63
integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]	1843.92		1.14326	235	1612.86
	2585.74	Low confidence	1.0433	578	2478.43
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	149.371	High confidence	1.10405	302	135.294
		Low confidence		398
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	3821.87	High confidence	1.01266	459	3774.08
	14153.3	Low confidence	1.03303	616	13700.7
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	3739.55	High confidence	1.01259	460	3693.07
	14251.4	Low confidence	1.03308	615	13795
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	1483.62	High confidence	1.01082	466	1467.74
		Low confidence		763
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	472.605	High confidence	1.4467	107	326.677
	2071.38	Low confidence	1.01489	722	2040.98
jm5 protein. [refseq;acc:nm_007075]	1099.49		1.1204	366	981.333
jumonji protein. [swissprot;acc:q92833]	17.5166		1751660	5	0.00001

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.