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

Results: HTML CSV LaTeX

Showing element 101 to 150 of 9634 in total

Value Type  : Ranked
Network Comparison Type  : Divided

Rank	description	Filtered	Interaction Map	network_comparison	green	red
26	cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318]	1	Low confidence	1.20085	238.454	286.347
	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	0	High confidence	1.60995	7533.33	12128.3
	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]		Low confidence	1.42223	6526.57	9282.29
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	1	High confidence	1.31818	44	58
27	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	0	Low confidence	1.41246	18516	13109
	cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973]	1		1.19792	237.743	284.798
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]		High confidence	1.31818	44	58
	ptd016 protein. [refseq;acc:nm_016125]	0		1.60673	11234	18050
28	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	1	Low confidence	1.19718	170	142
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]		High confidence	1.31416	153.671	201.949
	elongation of very long chain fatty acids protein 2. [swissprot;acc:q9nxb9]	0	Low confidence	1.40082	11505	16116.4
	p28 ing5. [refseq;acc:nm_032329]		High confidence	1.60337	7562.05	12124.8
29	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	1	Low confidence	1.19089	170.557	203.115
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	0	High confidence	1.57201	11625	7395
	solute carrier family 12 (potassium/chloride transporters), member 9; cation-chloride cotransporter-interacting protein. [refseq;acc:nm_020246]		Low confidence	1.39628	8687.07	12129.6
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	1	High confidence	1.29991	243.678	187.458
30	alpha 2 globin. [refseq;acc:nm_000517]	0	Low confidence	1.39185	15987.1	11486.2
	bcl2-related ovarian killer. [refseq;acc:nm_032515]	1		1.18995	223.235	265.638
	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	0	High confidence	1.57201	11625	7395
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]	1		1.29991	243.678	187.457
31	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]		Low confidence	1.17568	48.8186	57.395
	hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096]	0		1.39168	15984.3	11485.6
	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]		High confidence	1.53462	5266.67	8082.33
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005]	1		1.2999	243.677	187.458
32	importin 9. [refseq;acc:nm_018085]	0		1.52929	8691.76	13292.2
	myoglobin. [swissprot;acc:p02144]		Low confidence	1.39162	15983.3	11485.4
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	1		1.17505	232.49	273.188
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]		High confidence	1.29985	243.673	187.462
33	dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985]		Low confidence	1.17068	246.125	210.241
	fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344]	0		1.37827	14746.1	20324.1
	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]		High confidence	1.52929	8691.76	13292.2
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	1		1.28647	242.742	188.688
34	fibrillin 3. [refseq;acc:nm_032447]	0	Low confidence	1.37724	7506.66	5450.5
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]		High confidence	1.52196	17173.8	11284
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	Low confidence	1.16197	133.876	155.56
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]		High confidence	1.28235	242.453	189.07
35	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	0		1.5182	4871.6	3208.8
	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	1		1.27519	204.309	260.532
	protein tyrosine phosphatase type iva, member 2 isoform 1; protein tyrosine phosphatase iva2; protein tyrosine phosphatase iva; phosphatase of regenerating liver 2. [refseq;acc:nm_003479]	0	Low confidence	1.37553	16243	11808.5
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	1		1.14959	258.59	297.273
36	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]		High confidence	1.27519	204.309	260.532
	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	0		1.4984	14964	22422
	sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8]		Low confidence	1.37097	9520.8	13052.7
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	1		1.14906	258.33	296.837
37	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]			1.14874	217.843	250.244
	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	0	High confidence	1.49458	2582	3859
	myotubularin related protein 8. [refseq;acc:nm_017677]		Low confidence	1.36786	8993.6	12302
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	1	High confidence	1.27273	253	322
38	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	0		1.48976	10771	7230
	glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335]	1	Low confidence	1.14456	282.937	247.202

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.