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

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Showing element 401 to 450 of 77072 in total

Filtered  : 0
Interaction Map  : High confidence
Value Type  : Measured

network_comparison	green	Network Comparison Type	red	Rank	description
1.42539	112.25	Divided	160	112	lats homolog 1. [refseq;acc:nm_004690]
				113	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
1.43	2411.78	Subtracted	2410.35	491	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]
1.43747	2063	Divided	2965.5	111	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]
1.43863	2637		1833	110	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]
1.44	144		100	109	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]
1.44178	421		292	108	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]
1.4467	472.605		326.677	107	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]
1.45792	858.525		1251.66	106	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]
1.46454	2208.1		3233.86	105	fos-related antigen 2. [swissprot;acc:p15408]
1.46874	7500.75		5106.93	104	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]
1.47298	290.667		197.333	103	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854]
1.47595	977		1442	101	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]
				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	402		594	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]
1.48306	551.434		817.81	99	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]
1.48868	530		789	98	pp3111 protein. [refseq;acc:nm_022156]
1.52879	476.619		728.65	97	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]
1.54338	224.096		345.865	94	myosin vi. [swissprot;acc:q9um54]
1.54494	816.5		528.5	93	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]
1.56086	469.346		300.697	92	adp-ribosylation factor 3. [swissprot;acc:p16587]
1.56338	62.2106		39.7924	91	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]
1.57692	54.6667		34.6667	90	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]
1.58781	37.4843		23.6076	89	suppressor of actin 1. [refseq;acc:nm_014016]
1.58801	483.809		304.664	87	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]
				88	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]
1.61366	89.2447		55.3059	86	alpha crystallin a chain. [swissprot;acc:p02489]
1.62908	1106.88		679.449	85	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]
1.64478	1601.52		973.698	84	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]
1.64654	100.887		166.114	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]
1.65896	115.333		191.333	82	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]
1.66667	50		30	81	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]
1.68259	493		293	80	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765]
1.68316	544.991		323.79	79	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]
1.69474	95		161	78	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]
1.70956	416.524		712.071	77	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]
1.71403	183		313.667	76	dead-box protein. [refseq;acc:nm_018665]
1.71412	925.298		1586.07	75	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]
1.71473	859.34		501.151	74	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]
1.73233	37.693		65.2968	73	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]
1.73441	992.083		572	72	60s ribosomal protein l21. [swissprot;acc:p46778]
1.75762	352.75		620	71	ubiquitin protein ligase. [refseq;acc:nm_130466]
1.75947	1068		607	70	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]
1.7602	2804		1593	69	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]
1.76802	351.772		198.964	68	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]
1.78508	898		1603	67	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
1.78524	385.626		688.436	66	soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]
1.806	221.565	Subtracted	219.759	490	transcription factor btf3 homolog 3. [swissprot;acc:q13892]
1.80709	56.278	Divided	31.1429	63	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]
1.82385	384.407		210.767	62	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]

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.