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

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Showing element 401 to 450 of 77072 in total

Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence

network_comparison	Rank	description	green	red
1.47595	101	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	977	1442
	102	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]
1.47761	100	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]	402	594
1.48306	99	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]	551.434	817.81
1.48868	98	pp3111 protein. [refseq;acc:nm_022156]	530	789
1.52879	97	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]	476.619	728.65
1.54338	94	myosin vi. [swissprot;acc:q9um54]	224.096	345.865
1.54494	93	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	816.5	528.5
1.56086	92	adp-ribosylation factor 3. [swissprot;acc:p16587]	469.346	300.697
1.56338	91	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	62.2106	39.7924
1.57692	90	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	54.6667	34.6667
1.58781	89	suppressor of actin 1. [refseq;acc:nm_014016]	37.4843	23.6076
1.58801	87	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]	483.809	304.664
	88	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]
1.61366	86	alpha crystallin a chain. [swissprot;acc:p02489]	89.2447	55.3059
1.62908	85	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	1106.88	679.449
1.64478	84	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	1601.52	973.698
1.64654	83	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	100.887	166.114
1.65896	82	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	115.333	191.333
1.66667	81	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]	50	30
1.68259	80	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765]	493	293
1.68316	79	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	544.991	323.79
1.69474	78	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	95	161
1.70956	77	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	416.524	712.071
1.71403	76	dead-box protein. [refseq;acc:nm_018665]	183	313.667
1.71412	75	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	925.298	1586.07
1.71473	74	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]	859.34	501.151
1.73233	73	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	37.693	65.2968
1.73441	72	60s ribosomal protein l21. [swissprot;acc:p46778]	992.083	572
1.75762	71	ubiquitin protein ligase. [refseq;acc:nm_130466]	352.75	620
1.75947	70	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	1068	607
1.7602	69	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	2804	1593
1.76802	68	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	351.772	198.964
1.78508	67	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	898	1603
1.78524	66	soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	385.626	688.436
1.80709	63	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	56.278	31.1429
1.82385	62	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	384.407	210.767
1.82804	61	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	593.094	324.442
1.8441	60	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]	87.5499	47.4756
1.85328	59	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]	279.24	150.673
1.85588	58	40s ribosomal protein s26. [swissprot;acc:p02383]	81.2233	150.741
1.89769	57	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]	142.417	270.264
1.89874	56	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	142.981	271.484
1.92644	55	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	327.517	630.942
1.93484	54	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	330.189	638.862
2.05016	53	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	861.814	420.365
2.07438	52	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	481.725	999.28
2.0824	51	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	88.5622	184.422
2.09524	50	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	21	44
2.09722	49	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	151	72

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.