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

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Showing element 501 to 550 of 38536 in total

Network Comparison Type

: Divided

Rank	Value Type	description	Filtered	red	Interaction Map	network_comparison	green
32	Ranked	importin 9. [refseq;acc:nm_018085]	0	13292.2	High confidence	1.52929	8691.76
		myoglobin. [swissprot;acc:p02144]	0	11485.4	Low confidence	1.39162	15983.3
		protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	1	273.188	Low confidence	1.17505	232.49
		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]		187.462	High confidence	1.29985	243.673
	Squared	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]		9924.76	High confidence	2.53372	25146.6
		melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]		82347.8	Low confidence	1.33073	61881.5
		melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	0	3.41692	Low confidence	9.62112	0.355148
		phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	0	76.8994	High confidence	16.8159	4.57302
	Rooted	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	1	26.0288	High confidence	1.65937	43.1914
		melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	0	9.84765	Low confidence	1.69589	5.80678
		mitochondrial solute carrier protein. [refseq;acc:nm_145305]	1	145.551	Low confidence	1.1597	168.796
		ubiquitin protein ligase. [refseq;acc:nm_130466]	0	24.0391	High confidence	2.13529	11.258
33	Measured	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	1	1835.3		2.04611	896.972
		lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	0	12.6208		3.15402	39.8063
		melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	0	105.5	Low confidence	2.97183	35.5
		vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]	1	36360.3		1.19275	43368.8
	Ranked	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]	1	210.241		1.17068	246.125
		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]	0	20324.1		1.37827	14746.1
		nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	0	13292.2	High confidence	1.52929	8691.76
		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]	1	188.688		1.28647	242.742
	Squared	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	0	76.8994		16.8159	4.57302
		hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	1	82347.8	Low confidence	1.33073	61881.5
		melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	0	3.41692	Low confidence	9.62112	0.355148
		spermatogenesis associated 6. [refseq;acc:nm_019073]	1	9924.76	High confidence	2.53372	25146.6
	Rooted	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	0	12.3693	High confidence	2.0801	25.7294
		melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	0	9.84765	Low confidence	1.69589	5.80678
		protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	1	26.0288	High confidence	1.65937	43.1914
		retinoblastoma-associated factor 600. [refseq;acc:nm_020765]	1	76.5734	Low confidence	1.15738	88.6244
34	Measured	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	0	143	High confidence	3.04255	47
		guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	1	1836.71	High confidence	2.02382	907.546
		melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	0	105.5	Low confidence	2.97183	35.5
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	1	5339.5		1.1897	6352.4
	Ranked	fibrillin 3. [refseq;acc:nm_032447]	0	5450.5		1.37724	7506.66
		microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	0	11284	High confidence	1.52196	17173.8
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	155.56	Low confidence	1.16197	133.876
		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]		189.07	High confidence	1.28235	242.453
	Squared	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]		9924.76		2.53372	25146.6
		lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	0	0.0435834		15.9968	0.697197
		melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	1	82347.8	Low confidence	1.33073	61881.5
		melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	0	3.41692	Low confidence	9.62112	0.355148
	Rooted	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	1	40.2812	High confidence	1.65305	24.3678
		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	0	9.84765	Low confidence	1.69589	5.80678
		phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	0	23.8747	High confidence	2.02503	11.7898
		putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]	1	49.0544	Low confidence	1.15698	56.755
35	Measured	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	0	459.5	High confidence	2.99674	1377
		deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	1	33111.4	Low confidence	1.18866	39358.1
		guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	1	1836.71	High confidence	2.02378	907.564
		melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	0	105.5	Low confidence	2.97183	35.5
	Ranked	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	0	3208.8	High confidence	1.5182	4871.6
	Ranked	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	1	260.532	High confidence	1.27519	204.309

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/