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

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Showing element 5308 to 5357 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
2654	nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653]	Divided	201.452	201.674	1.0011
2655	b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749]		201.445	201.667
	probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1]	Subtracted	194.097	194.328	0.231
2656	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902]	Divided	217.179	216.943	1.00109
	thioredoxin domain containing; thioredoxin-related transmembrane protein; thioredoxin domain-containing. [refseq;acc:nm_030755]	Subtracted	210.136	209.911	0.225
2657	channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700]	Divided	216.934	216.7	1.00108
	nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221]	Subtracted	201.37	201.594	0.224
2658	nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838]		201.451	201.673	0.222
	presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [swissprot;acc:p78352]	Divided	216.933	216.7	1.00108
2659	nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [swissprot;acc:q15653]	Subtracted	201.452	201.674	0.222
	presynaptic protein sap102 (synapse-associated protein 102) (neuroendocrine-dlg) (ne-dlg) (discs, large homolog 3). [swissprot;acc:q92796]	Divided	216.933	216.7	1.00108
2660	nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653]	Subtracted	201.452	201.674	0.222
	presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959]	Divided	216.937	216.704	1.00108
2661	b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749]	Subtracted	201.445	201.667	0.222
	proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332]	Divided	204.768	204.549	1.00107
2662	glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695]	Subtracted	214.575	214.354	0.221
	molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007]	Divided	204.768	204.549	1.00107
2663	anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885]
	similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6]	Subtracted	216.288	216.067	0.221
2664	60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914]	Divided	204.768	204.549	1.00107
	proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332]	Subtracted			0.219
2665	pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989]		166.612	166.393
	proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591]	Divided	204.768	204.549	1.00107
2666	molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007]	Subtracted			0.219
	thioredoxin domain containing; thioredoxin-related transmembrane protein; thioredoxin domain-containing. [refseq;acc:nm_030755]	Divided	210.136	209.911	1.00107
2667	anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885]	Subtracted	204.768	204.549	0.219
	molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396]	Divided			1.00107
2668	60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914]	Subtracted			0.219
	fuse binding protein 3 (fragment). [sptrembl;acc:q92946]	Divided	217.176	216.944	1.00107
2669	glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695]		214.575	214.354	1.00103
	proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591]	Subtracted	204.768	204.549	0.219
2670	molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396]
	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]	Divided	144.391	144.538	1.00102
2671	rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [refseq;acc:nm_004584]	Subtracted	216.372	216.588	0.216
	similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6]	Divided	216.288	216.067	1.00102
2672	branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687]		210.957	210.741
		Subtracted			0.216
2673	28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8]		214.893	215.108	0.215
	rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [refseq;acc:nm_004584]	Divided	216.372	216.588	1.001
2674	enhancer of rudimentary homolog. [swissprot;acc:q14259]	Subtracted	214.893	215.108	0.215
	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104]	Divided	203.151	202.948	1.001
2675	28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8]		214.893	215.108
	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104]	Subtracted	203.151	202.948	0.203
2676	enhancer of rudimentary homolog. [swissprot;acc:q14259]	Divided	214.893	215.108	1.001
	proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436]	Subtracted	219.829	219.629	0.2
2677	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]	Divided	144.412	144.553	1.00098
	nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [swissprot;acc:p16991]	Subtracted	208.438	208.635	0.197
2678	dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989]
	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]	Divided	144.411	144.552	1.00098
2679	anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366]		190.142	189.959	1.00096

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.