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

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Showing element 901 to 950 of 38536 in total

Filtered  : 0
Network Comparison Type  : Divided

Rank	description	network_comparison	Value Type	green	Interaction Map	red
113	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	1.19816	Ranked	6797.56	High confidence	5673.33
	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503]	1.37179	Measured	78	Low confidence	107
	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	1.42539		112.25	High confidence	160
	ubiquinol-cytochrome c reductase complex 7.2 kda protein (ec 1.10.2.2) (cytochrome c1, nonheme 7 kda protein) (complex iii subunit x) (7.2 kda cytochrome c1-associated protein subunit) (hspc119). [swissprot;acc:q9udw1]	1.91901	Squared	61.9262	Low confidence	118.837
114	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]	1.19525	Ranked	10603.2	High confidence	8871.11
	calponin h2, smooth muscle (neutral calponin). [swissprot;acc:q99439]	1.36592	Measured	1049.11	Low confidence	768.061
	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]	1.4204		472.945	High confidence	671.769
	laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942]	1.25192	Rooted	6.96791	Low confidence	8.7233
	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	1.27009		18.7165	High confidence	14.7363
	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]	1.90678	Squared	5.9911	Low confidence	11.4237
	transcription factor tel-2 (ets-related protein tel2) (tel related ets factor). [swissprot;acc:q9y603]	1.20024	Ranked	9278.67		7730.67
	zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]	1.9892	Squared	69.7867	High confidence	35.0828
115	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	1.97772		53.4024		105.615
	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	1.25054	Rooted	17.542	Low confidence	14.0275
	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	1.26912		14.5738	High confidence	18.4959
	g protein-coupled receptor kinase grk5 (ec 2.7.1.-) (g-protein-coupled receptor kinase 5). [swissprot;acc:p34947]	1.3561	Measured	410	Low confidence	556
	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	1.88694	Squared	16.8625		31.8185
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	1.19952	Ranked	12255.4		10216.9
	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	1.19427		15627	High confidence	18662.8
	zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]	1.41039	Measured	543		385
116	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	1.40632		475		668
	dead-box protein. [refseq;acc:nm_018665]	1.94853	Squared	19.3759		37.7545
	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	1.26202	Rooted	7.75282		9.7842
	g protein-coupled receptor kinase grk6 (ec 2.7.1.-) (g-protein-coupled receptor kinase 6). [swissprot;acc:p43250]	1.3561	Measured	410	Low confidence	556
	metaxin 1. [swissprot;acc:q13505]	1.19335	Ranked	16422.1	High confidence	13761.3
	rna transcribed from l1 repetitive element (shr4) (fragment). [sptrembl;acc:q9y443]	1.25	Rooted	31.225	Low confidence	24.98
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	1.19816	Ranked	6797.56		5673.33
	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503]	1.88182	Squared	1.44		2.70982
117	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	1.19285	Ranked	13771.5	High confidence	11545
	helicase/primase complex protein. [refseq;acc:nm_138336]	1.35238	Measured	210	Low confidence	284
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	1.26131	Rooted	33.5888	High confidence	26.63
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	1.19559	Ranked	13288.7	Low confidence	11114.8
	putative p150. [sptrembl;acc:o00370]	1.25	Rooted	31.225		24.98
	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	1.93793	Squared	1.05706	High confidence	0.545459
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	1.39754	Measured	122		170.5
		1.88086	Squared	18724.4	Low confidence	9955.21
118	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	1.19269	Ranked	14370.7	High confidence	12049
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	1.87909	Squared	9366.63	Low confidence	4984.65
	lamin-like protein in hindiii repetitive element derived dna, 3' end (fragment). [sptrembl;acc:q14755]	1.25	Rooted	31.225		24.98
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	1.19504	Ranked	9652.56		11535.2
	methyltransferase like 2. [refseq;acc:nm_018396]	1.3871	Measured	43	High confidence	31
	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	1.25851	Rooted	11.4849		9.1258
	signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]	1.92813	Squared	124.83		240.689
	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]	1.3506	Measured	113	Low confidence	83.6667
119	cdc42-binding protein kinase beta; cdc42-binding protein kinase beta (dmpk-like); mrck beta; dmpk-like. [refseq;acc:nm_006035]	1.18962	Ranked	4873		5797
	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	1.37734	Measured	460.2	High confidence	633.85
	line-1 reverse transcriptase (fragment). [sptrembl;acc:o00172]	1.25	Rooted	31.225	Low confidence	24.98
	mesoderm induction early response 1. [refseq;acc:nm_020948]	1.19216	Ranked	4302.5	High confidence	3609
	methyltransferase like 2. [refseq;acc:nm_018396]	1.92403	Squared	0.437633		0.227456
	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	1.33918	Measured	60.8613	Low confidence	81.504

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.