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

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Showing element 501 to 550 of 38536 in total

Network Comparison Type

: Divided

Rank	Filtered	green	Interaction Map	network_comparison	description	Value Type	red
32	0	35.5	Low confidence	2.97183	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Measured	105.5
		184	High confidence	3.25	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	Measured	598
		8691.76	High confidence	1.52929	importin 9. [refseq;acc:nm_018085]	Ranked	13292.2
		15983.3	Low confidence	1.39162	myoglobin. [swissprot;acc:p02144]	Ranked	11485.4
	1	43.1914	High confidence	1.65937	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Rooted	26.0288
		168.796	Low confidence	1.1597	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted	145.551
		232.49	Low confidence	1.17505	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Ranked	273.188
		243.673	High confidence	1.29985	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]	Ranked	187.462
		895.893		2.04793	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Measured	1834.73
		25146.6		2.53372	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Squared	9924.76
		43368.8	Low confidence	1.19275	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured	36360.3
		61881.5		1.33073	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Squared	82347.8
33	0	0.355148		9.62112	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]		3.41692
		4.57302	High confidence	16.8159	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]		76.8994
		5.80678	Low confidence	1.69589	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Rooted	9.84765
		25.7294	High confidence	2.0801	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Rooted	12.3693
		35.5	Low confidence	2.97183	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Measured	105.5
		39.8063	High confidence	3.15402	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Measured	12.6208
		8691.76	High confidence	1.52929	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	Ranked	13292.2
		14746.1	Low confidence	1.37827	fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344]	Ranked	20324.1
	1	43.1914	High confidence	1.65937	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Rooted	26.0288
		88.6244	Low confidence	1.15738	retinoblastoma-associated factor 600. [refseq;acc:nm_020765]	Rooted	76.5734
		242.742	High confidence	1.28647	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	Ranked	188.688
		246.125	Low confidence	1.17068	dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985]	Ranked	210.241
		896.972	High confidence	2.04611	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	Measured	1835.3
		25146.6	High confidence	2.53372	spermatogenesis associated 6. [refseq;acc:nm_019073]	Squared	9924.76
		43368.8	Low confidence	1.19275	vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]	Measured	36360.3
		61881.5		1.33073	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Squared	82347.8
34	0	0.355148		9.62112	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]		3.41692
		0.697197	High confidence	15.9968	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]		0.0435834
		5.80678	Low confidence	1.69589	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Rooted	9.84765
		11.7898	High confidence	2.02503	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Rooted	23.8747
		35.5	Low confidence	2.97183	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Measured	105.5
		47	High confidence	3.04255	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	Measured	143
		7506.66	Low confidence	1.37724	fibrillin 3. [refseq;acc:nm_032447]	Ranked	5450.5
		17173.8	High confidence	1.52196	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	Ranked	11284
	1	24.3678	High confidence	1.65305	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	Rooted	40.2812
		56.755	Low confidence	1.15698	putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]	Rooted	49.0544
		133.876	Low confidence	1.16197	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked	155.56
		242.453	High confidence	1.28235	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]	Ranked	189.07
		907.546	High confidence	2.02382	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	Measured	1836.71
		6352.4	Low confidence	1.1897	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Measured	5339.5
		25146.6	High confidence	2.53372	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	Squared	9924.76
		61881.5	Low confidence	1.33073	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]		82347.8
35	0	0.355148		9.62112	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]		3.41692
		5.80678		1.69589	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Rooted	9.84765
		11.7898	High confidence	2.02503	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Rooted	23.8747
		35.5	Low confidence	2.97183	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Measured	105.5
		647.816	High confidence	12.7767	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	Squared	50.7031
		1377	High confidence	2.99674		Measured	459.5

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/