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

Results: HTML CSV LaTeX

Showing element 401 to 450 of 29840 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	Value Type	description	red	Filtered	network_comparison	green
51	Measured	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	779.167	1	1.78438	1390.33
		ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	184.422	0	2.0824	88.5622
	Ranked	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	7168		1.40494	5102
		spermatogenesis associated 6. [refseq;acc:nm_019073]	133	1	1.26667	105
	Squared	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]	0.872309	0	4.58475	3.99932
		associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	28994.2	1	1.69212	17134.8
	Rooted	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	27.7254		1.58807	44.0299
		nanos (fragment). [sptrembl;acc:q8wy41]	19.4165	0	1.58009	12.2882
52	Measured	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	779.167	1	1.78438	1390.33
		dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	999.28	0	2.07438	481.725
	Ranked	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	133	1	1.26667	105
		ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]	3284	0	1.38688	4554.5
	Squared	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	28994.2	1	1.69212	17134.8
		selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	1.22698	0	4.39835	5.39669
	Rooted	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	16.3095		1.55718	25.3969
		neuralized-like. [refseq;acc:nm_004210]	27.9107	1	1.58239	44.1656
53	Measured	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]	779.167		1.78438	1390.33
		muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	420.365	0	2.05016	861.814
	Ranked	transcription factor jun-b. [swissprot;acc:p17275]	201.144	1	1.26611	158.868
		ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966]	3284	0	1.38688	4554.5
	Squared	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	28994.2	1	1.69212	17134.8
		transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	0.458225	0	4.39001	0.104379
	Rooted	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	11.844		1.5213	18.0183
		nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181]	30.8986	1	1.50369	46.4619
54	Measured	deltex 2. [refseq;acc:nm_020892]	1618.84		1.63814	2651.88
		formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	638.862	0	1.93484	330.189
	Ranked	syntaxin 10 (syn10). [swissprot;acc:o60499]	13884.4		1.36949	19014.6
		transcription factor jun-d. [swissprot;acc:p17535]	200.941	1	1.26425	158.941
	Squared	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	219048		1.68808	129762
		soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	295.992	0	4.28286	69.1109
	Rooted	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	14.8299		1.52033	22.5463
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	40.0958	1	1.46645	58.7986
55	Measured	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	1629.21		1.63399	2662.12
		huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	630.942	0	1.92644	327.517
	Ranked	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	320.927	1	1.26134	254.434
		sedlin. [swissprot;acc:o14582]	22440	0	1.36929	16388
	Squared	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	468.221		4.14293	113.017
		hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	219048	1	1.68808	129762
	Rooted	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	24.4683	0	1.50287	16.281
		potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	41.6734	1	1.44038	28.9323
56	Measured	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	1631.67		1.63302	2664.55
		tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	271.484	0	1.89874	142.981
	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	266.856	1	1.25998	336.233
		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	22440	0	1.36929	16388
	Squared	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	219048	1	1.68808	129762
		ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	15.4957	0	4.04283	3.83288
	Rooted	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	41.6851	1	1.43986	28.9509
		protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	11.2068	0	1.49604	16.7658
57	Measured	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]	270.264		1.89769	142.417
		kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	1631.67	1	1.63302	2664.55

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.