Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 Interaction Map Network Comparison Type network_comparison Value Type red Filtered green

Results: HTML CSV LaTeX

Showing element 401 to 450 of 14920 in total

Interaction Map

: High confidence
Network Comparison Type

: Divided

Rank	description	network_comparison	Value Type	red	Filtered	green
51	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]	4.58475	Squared	0.872309	0	3.99932
	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	1.69212	Squared	28994.2	1	17134.8
	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	1.40494	Ranked	7168	0	5102
	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	1.58807	Rooted	27.7254	1	44.0299
	nanos (fragment). [sptrembl;acc:q8wy41]	1.58009	Rooted	19.4165	0	12.2882
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	1.78438	Measured	779.167	1	1390.33
	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	2.0824	Measured	184.422	0	88.5622
	spermatogenesis associated 6. [refseq;acc:nm_019073]	1.26667	Ranked	133	1	105
52	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	1.26667		133	1	105
	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]	1.38688		3284	0	4554.5
	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	1.78438	Measured	779.167	1	1390.33
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	2.07438	Measured	999.28	0	481.725
	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]	1.55718	Rooted	16.3095	0	25.3969
	neuralized-like. [refseq;acc:nm_004210]	1.58239	Rooted	27.9107	1	44.1656
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	1.69212	Squared	28994.2	1	17134.8
	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	4.39835	Squared	1.22698	0	5.39669
53	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	1.5213	Rooted	11.844	0	18.0183
	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]	1.78438	Measured	779.167	1	1390.33
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	2.05016	Measured	420.365	0	861.814
	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]	1.50369	Rooted	30.8986	1	46.4619
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	1.69212	Squared	28994.2	1	17134.8
	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	4.39001	Squared	0.458225	0	0.104379
	transcription factor jun-b. [swissprot;acc:p17275]	1.26611	Ranked	201.144	1	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]	1.38688	Ranked	3284	0	4554.5
54	deltex 2. [refseq;acc:nm_020892]	1.63814	Measured	1618.84	1	2651.88
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	1.93484	Measured	638.862	0	330.189
	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	1.52033	Rooted	14.8299	0	22.5463
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	1.68808	Squared	219048	1	129762
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	1.46645	Rooted	40.0958	1	58.7986
	soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	4.28286	Squared	295.992	0	69.1109
	syntaxin 10 (syn10). [swissprot;acc:o60499]	1.36949	Ranked	13884.4	0	19014.6
	transcription factor jun-d. [swissprot;acc:p17535]	1.26425	Ranked	200.941	1	158.941
55	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	1.50287	Rooted	24.4683	0	16.281
		1.63399	Measured	1629.21	1	2662.12
		4.14293	Squared	468.221	0	113.017
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	1.68808	Squared	219048	1	129762
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	1.92644	Measured	630.942	0	327.517
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	1.44038	Rooted	41.6734	1	28.9323
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	1.26134	Ranked	320.927	1	254.434
	sedlin. [swissprot;acc:o14582]	1.36929	Ranked	22440	0	16388
56	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	1.43986	Rooted	41.6851	1	28.9509
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	1.25998	Ranked	266.856		336.233
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	1.68808	Squared	219048		129762
	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	1.49604	Rooted	11.2068	0	16.7658
	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	4.04283	Squared	15.4957		3.83288
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	1.36929	Ranked	22440		16388
	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]	1.63302	Measured	1631.67	1	2664.55
	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	1.89874		271.484	0	142.981
57	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]	1.89769		270.264		142.417
57	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	4.03837	Squared	0.849445		3.43037

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.

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