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 network_comparison Interaction Map description Value Type red Network Comparison Type

Results: HTML CSV LaTeX

Showing element 501 to 550 of 38536 in total

Network Comparison Type

: Divided

Rank	Filtered	green	network_comparison	Interaction Map	description	Value Type	red
32	0	35.5	2.97183	Low confidence	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Measured	105.5
		184	3.25	High confidence	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	Measured	598
		8691.76	1.52929	High confidence	importin 9. [refseq;acc:nm_018085]	Ranked	13292.2
		15983.3	1.39162	Low confidence	myoglobin. [swissprot;acc:p02144]	Ranked	11485.4
	1	43.1914	1.65937	High confidence	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	1.1597	Low confidence	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted	145.551
		232.49	1.17505	Low confidence	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	1.29985	High confidence	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	1.19275	Low confidence	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	16.8159	High confidence	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]		76.8994
		5.80678	1.69589	Low confidence	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Rooted	9.84765
		25.7294	2.0801	High confidence	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	2.97183	Low confidence	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Measured	105.5
		39.8063	3.15402	High confidence	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Measured	12.6208
		8691.76	1.52929	High confidence	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	Ranked	13292.2
		14746.1	1.37827	Low confidence	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	1.65937	High confidence	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	1.15738	Low confidence	retinoblastoma-associated factor 600. [refseq;acc:nm_020765]	Rooted	76.5734
		242.742	1.28647	High confidence	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	1.17068	Low confidence	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	2.04611	High confidence	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	Measured	1835.3
		25146.6	2.53372	High confidence	spermatogenesis associated 6. [refseq;acc:nm_019073]	Squared	9924.76
		43368.8	1.19275	Low confidence	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	15.9968	High confidence	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]		0.0435834
		5.80678	1.69589	Low confidence	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Rooted	9.84765
		11.7898	2.02503	High confidence	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Rooted	23.8747
		35.5	2.97183	Low confidence	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Measured	105.5
		47	3.04255	High confidence	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	Measured	143
		7506.66	1.37724	Low confidence	fibrillin 3. [refseq;acc:nm_032447]	Ranked	5450.5
		17173.8	1.52196	High confidence	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	1.65305	High confidence	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	Rooted	40.2812
		56.755	1.15698	Low confidence	putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]	Rooted	49.0544
		133.876	1.16197	Low confidence	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked	155.56
		242.453	1.28235	High confidence	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	2.02382	High confidence	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	Measured	1836.71
		6352.4	1.1897	Low confidence	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Measured	5339.5
		25146.6	2.53372	High confidence	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	Squared	9924.76
		61881.5	1.33073	Low confidence	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	2.02503	High confidence	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Rooted	23.8747
		35.5	2.97183	Low confidence	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Measured	105.5
		647.816	12.7767	High confidence	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	Squared	50.7031
		1377	2.99674	High confidence		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/