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

Results: HTML CSV LaTeX

Showing element 401 to 450 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
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]	Squared	0	0.872309	3.99932	4.58475
	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Squared	1	28994.2	17134.8	1.69212
	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	Ranked	0	7168	5102	1.40494
	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Rooted	1	27.7254	44.0299	1.58807
	nanos (fragment). [sptrembl;acc:q8wy41]	Rooted	0	19.4165	12.2882	1.58009
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Measured	1	779.167	1390.33	1.78438
	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	Measured	0	184.422	88.5622	2.0824
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Ranked	1	133	105	1.26667
52	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]		1	133	105	1.26667
	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]		0	3284	4554.5	1.38688
	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Measured	1	779.167	1390.33	1.78438
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Measured	0	999.28	481.725	2.07438
	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]	Rooted	0	16.3095	25.3969	1.55718
	neuralized-like. [refseq;acc:nm_004210]	Rooted	1	27.9107	44.1656	1.58239
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Squared	1	28994.2	17134.8	1.69212
	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	Squared	0	1.22698	5.39669	4.39835
53	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Rooted	0	11.844	18.0183	1.5213
	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]	Measured	1	779.167	1390.33	1.78438
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	Measured	0	420.365	861.814	2.05016
	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]	Rooted	1	30.8986	46.4619	1.50369
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Squared	1	28994.2	17134.8	1.69212
	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	Squared	0	0.458225	0.104379	4.39001
	transcription factor jun-b. [swissprot;acc:p17275]	Ranked	1	201.144	158.868	1.26611
	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]	Ranked	0	3284	4554.5	1.38688
54	deltex 2. [refseq;acc:nm_020892]	Measured	1	1618.84	2651.88	1.63814
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Measured	0	638.862	330.189	1.93484
	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	Rooted	0	14.8299	22.5463	1.52033
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Squared	1	219048	129762	1.68808
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Rooted	1	40.0958	58.7986	1.46645
	soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	Squared	0	295.992	69.1109	4.28286
	syntaxin 10 (syn10). [swissprot;acc:o60499]	Ranked	0	13884.4	19014.6	1.36949
	transcription factor jun-d. [swissprot;acc:p17535]	Ranked	1	200.941	158.941	1.26425
55	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Measured	1	1629.21	2662.12	1.63399
		Squared	0	468.221	113.017	4.14293
		Rooted	0	24.4683	16.281	1.50287
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Squared	1	219048	129762	1.68808
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Measured	0	630.942	327.517	1.92644
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Rooted	1	41.6734	28.9323	1.44038
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Ranked	1	320.927	254.434	1.26134
	sedlin. [swissprot;acc:o14582]	Ranked	0	22440	16388	1.36929
56	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	Rooted	1	41.6851	28.9509	1.43986
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Ranked		266.856	336.233	1.25998
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Squared		219048	129762	1.68808
	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	Rooted	0	11.2068	16.7658	1.49604
	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	Squared		15.4957	3.83288	4.04283
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Ranked		22440	16388	1.36929
	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]	Measured	1	1631.67	2664.55	1.63302
	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]		0	271.484	142.981	1.89874
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]			270.264	142.417	1.89769
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]	Squared		0.849445	3.43037	4.03837

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.

- http://analysis.yellowcouch.org/