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	Network Comparison Type	Value Type	Interaction Map	Filtered	green	red	network_comparison

Results: HTML CSV LaTeX

Showing element 263 to 312 of 6456 in total

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

Rank	description	Network Comparison Type	green	red	network_comparison
132	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Subtracted	196.695	229.406	32.711
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Divided	290	350	1.2069
133	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Subtracted	194.72	226.887	32.167
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Divided	290	350	1.2069
134	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Subtracted	194.79	226.884	32.094
135	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Divided	290	350	1.2069
	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Subtracted	231.407	263.215	31.808
136	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Divided	290	350	1.2069
	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Subtracted	231.407	263.215	31.808
137	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]		231.394	263.191	31.797
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Divided	290	350	1.2069
138	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	Subtracted	205.556	174.667	30.889
	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	Divided	234.204	194.372	1.20493
139	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]		225.68	271.752	1.20415
	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	Subtracted	256.835	287.41	30.575
140	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]		198.011	228.306	30.295
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Divided	49	59	1.20408
141	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Subtracted	269.238	239.991	29.247
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Divided	49	59	1.20408
142	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]
	thrombospondin 3 precursor. [swissprot;acc:p49746]	Subtracted	269.234	239.99	29.244
143	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	Divided	49	59	1.20408
	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	Subtracted	211.382	240.133	28.751
144	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]		267.915	239.35	28.565
	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Divided	319.651	265.686	1.20312
145	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Subtracted	267.881	239.336	28.545
	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Divided	319.546	265.639	1.20293
146	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]		319.531	265.632	1.20291
	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	Subtracted	267.879	239.336	28.543
147	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]		267.842	239.32	28.522
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Divided	42.3003	50.7983	1.2009
148	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]	Subtracted	198.444	226.582	28.138
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Divided	247.559	296.677	1.19841
149	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]		170	142	1.19718
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Subtracted	198.444	226.582	28.138
150	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Divided	46	55	1.19565
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Subtracted	198.444	226.582	28.138
151	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Divided	46	55	1.19565
	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	Subtracted	198.444	226.582	28.138
152	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Divided	46	55	1.19565
	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	Subtracted	198.444	226.582	28.138
153	chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]	Divided	298.263	249.663	1.19466
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Subtracted	198.444	226.582	28.138
154	musashi 2 isoform a. [refseq;acc:nm_138962]		199.458	227.491	28.033
	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]	Divided	298.263	249.663	1.19466
155	musashi 1. [refseq;acc:nm_002442]	Subtracted	199.458	227.491	28.033
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Divided	298.263	249.663	1.19466
156	nuclear protein ukp68. [refseq;acc:nm_024824]	Subtracted	199.458	227.491	28.033
	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081]	Divided	298.263	249.663	1.19466

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.