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

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Showing element 2875 to 2924 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
360	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Ranked	0	16321	15577	1.04776
		Squared		0.545325	0.615621	1.12891
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Measured		48	51	1.0625
	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	Rooted	1	49.3771	54.5905	1.10558
	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	Ranked		243.072	266.559	1.09663
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]	Squared		9814.47	7911.48	1.24054
361	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	Rooted		50.7801	45.9472	1.10518
	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	Measured		12787.6	10880.5	1.17528
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Rooted	0	27.5221	28.7585	1.04492
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Ranked		16321	15577	1.04776
		Squared		0.545325	0.615621	1.12891
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Measured		48	51	1.0625
	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	Ranked	1	242.83	266.248	1.09644
	splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246]	Squared		70694.1	56989.9	1.24047
362	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	Rooted		50.7803	45.9477	1.10518
	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Rooted	0	27.5242	28.7604	1.04491
	apical-like protein (apxl protein). [swissprot;acc:q13796]	Ranked	1	231.492	211.136	1.09641
	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	Measured	1	12786.6	10879.9	1.17525
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Ranked	0	16321	15577	1.04776
		Squared		0.545325	0.615621	1.12891
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Measured		48	51	1.0625
	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	Squared	1	57808.9	46630.3	1.23973
363	60s ribosomal protein l18a. [swissprot;acc:q02543]	Rooted	0	30.8547	32.2238	1.04437
	block of proliferation 1. [swissprot;acc:q14137]	Rooted	1	49.4884	54.6735	1.10477
	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	Measured	1	12780.7	10876.4	1.17509
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Measured	0	48	51	1.0625
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Ranked		16321	15577	1.04776
		Squared		0.545325	0.615621	1.12891
	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Ranked	1	231.481	211.131	1.09639
	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885]	Squared		57579.2	46497.2	1.23834
364	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	Rooted		50.0785	55.3215	1.1047
	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	Ranked		243.208	266.617	1.09625
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Measured	0	48	51	1.0625
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	Ranked		16321	15577	1.04776
		Squared		0.545325	0.615621	1.12891
	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	Measured	1	5189	6088.47	1.17334
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Squared	1	17957.2	22234.1	1.23817
	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	Rooted	0	53.8642	56.248	1.04426
365	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	Ranked	1	242.744	266.07	1.09609
	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Squared		17965.8	22243	1.23807
	calcyphosine. [swissprot;acc:q13938]	Measured		5189	6088.47	1.17334
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Rooted	0	30.3712	31.6971	1.04366
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Measured	0	48	51	1.0625
	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	Rooted	1	49.7541	54.9425	1.10428
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Ranked	0	7769.96	8139.71	1.04759
	tubby protein homolog. [swissprot;acc:p50607]	Squared	0	9661.54	10902.9	1.12848
366	40s ribosomal protein s15a. [swissprot;acc:p39027]	Rooted	1	50.5463	45.7763	1.1042
	40s ribosomal protein s5. [swissprot;acc:p46782]	Ranked		242.473	265.756	1.09602
	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	Squared		62783.5	50784.1	1.23628
	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	Measured		5189	6088.47	1.17334

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/