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

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Showing element 12864 to 12913 of 29840 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	green	red	network_comparison
2200	insulin gene enhancer protein isl-2 (islet-2). [swissprot;acc:q96a47]	Divided	195.466	196.748	1.00656
2201	3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952]	Subtracted	208.162	209.54	1.378
	p47 protein isoform a. [refseq;acc:nm_016143]	Divided	212.254	213.642	1.00654
2202	tumor susceptibility gene 101 protein. [swissprot;acc:q99816]		194.7	195.97	1.00652
	zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]	Subtracted	208.162	209.54	1.378
2203	bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885]		224.337	222.959
	symplekin. [swissprot;acc:q92797]	Divided	163.8	162.741	1.00651
2204	ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [swissprot;acc:q9y230]		220.8	219.377	1.00649
	testis-specific bromodomain protein. [refseq;acc:nm_001726]	Subtracted	224.336	222.958	1.378
2205	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]	Divided	200.413	199.129	1.00645
	hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [refseq;acc:nm_004507]	Subtracted	208.162	209.54	1.378
2206	hyaluronan binding protein 4; intracellular antigen detected by monoclonal antibody ki-1; intracellular hyaluronan-binding protein; chromodomain helicase dna binding protein 3 interacting protein. [refseq;acc:nm_014282]
	transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [swissprot;acc:p55072]	Divided	214.19	215.571	1.00645
2207	nag14 protein. [refseq;acc:nm_022143]	Subtracted	224.337	222.959	1.378
	sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864]	Divided	200.413	199.129	1.00645
2208	clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172]
	prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [swissprot;acc:p13674]	Subtracted	208.162	209.54	1.378
2209	atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450]	Divided	200.413	199.129	1.00645
	homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786]	Subtracted	208.162	209.54	1.378
2210	lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [swissprot;acc:o00754]	Divided	200.413	199.129	1.00645
	rad1 homolog isoform 1; exonuclease homolog rad1; cell cycle checkpoint protein rad1 a/b; rad1-like protein; cell cycle checkpoint protein hrad1; dna repair exonuclease (rec1); dna repair protein rad1; rad1-like dna damage checkpoint protein. [refseq;acc:nm_002853]	Subtracted	208.162	209.54	1.378
2211	bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440]		224.338	222.96
	rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]	Divided	200.413	199.129	1.00645
2212	28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3]		225.854	224.411	1.00643
	prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [swissprot;acc:o15460]	Subtracted	208.162	209.54	1.378
2213	dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475]	Divided	211.475	210.127	1.00642
	mitochondrial ribosomal protein l18. [refseq;acc:nm_014161]	Subtracted	224.943	223.58	1.363
2214	fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090]	Divided	220.108	221.509	1.00637
	vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065]	Subtracted	198.71	200.063	1.353
2215	43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702]		214.194	215.547
	fatty acid-binding protein, epidermal (e-fabp) (psoriasis-associated fatty acid-binding protein homolog) (pa-fabp). [swissprot;acc:q01469]	Divided	220.108	221.509	1.00637
2216	fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540]
	vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763]	Subtracted	198.71	200.063	1.353
2217	vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379]
	wd-repeat protein 4. [swissprot;acc:p57081]	Divided	220.108	221.509	1.00637
2218	cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735]	Subtracted	198.71	200.063	1.353
	myelin p2 protein. [swissprot;acc:p02689]	Divided	220.108	221.509	1.00637
2219	adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3]	Subtracted	198.71	200.063	1.353
	kelch-like protein 8. [swissprot;acc:q9p2g9]	Divided	220.108	221.509	1.00637
2220	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]
	vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836]	Subtracted	198.71	200.063	1.353
2221	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Divided	220.108	221.509	1.00637
	dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475]	Subtracted	211.475	210.127	1.348
2222	beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429]	Divided	220.108	221.509	1.00637
	nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570]	Subtracted	213.153	211.81	1.343
2223	fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413]	Divided	220.108	221.509	1.00637
	kinesin-like protein kif3c. [swissprot;acc:o14782]	Subtracted	220.377	219.045	1.332
2224	kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066]		220.371	219.047	1.324
	retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329]	Divided	220.108	221.509	1.00637
2225	indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050]

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.