MK5 Microarray Data

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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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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 2680 to 2729 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
168	lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]	Squared	Divided	0	338.863	213.584	1.58656
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Measured		1	23693.7	18263	1.29736
	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031]	Rooted		0	43.2078	37.3703	1.15621
	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Squared		1	173408	242989	1.40126
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Rooted	Subtracted		55.6161	66.7332	11.1171
	serpin b12. [swissprot;acc:q96p63]	Measured		0	199.549	5.56738	193.982
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Rooted			18.9056	15.8624	3.0432
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]		Divided	1	56.3709	65.8949	1.16895
	transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525]	Measured		0	334.012	420.355	1.2585
169	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	Ranked			9875.43	11256.8	1.13988
	apg3p; pc3-96 protein. [refseq;acc:nm_022488]			1	82.5916	98.0548	1.18722
	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653]	Rooted			62.762	53.7761	1.1671
	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]	Ranked	Subtracted		312	284	28
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Measured			4245.52	5942.75	1697.23
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]		Divided	0	244	194	1.25773
		Squared			14.0914	8.90793	1.58189
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Measured	Subtracted		199.249	5.71669	193.532
	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	Rooted			25.0015	28.0435	3.042
	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]		Divided		6.48074	7.48331	1.1547
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Measured		1	23693.7	18263	1.29736
	pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148]	Squared	Subtracted		69165	52991.7	16173.3
	pp3111 protein. [refseq;acc:nm_022156]	Ranked		0	6185	7603	1418
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Rooted		1	55.6161	66.7332	11.1171
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Squared		0	1914.2	1419.67	494.53
	symplekin. [swissprot;acc:q92797]		Divided	1	124118	88668.8	1.39979
170	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	Measured	Subtracted	0	668	475	193
	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]	Squared		1	69165	52991.7	16173.3
	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	Rooted	Divided		53.4993	45.9227	1.16499
	calcyphosine. [swissprot;acc:q13938]	Squared		0	175.528	276.854	1.57726
	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857]			1	96730.5	69286.7	1.39609
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Ranked	Subtracted		227.971	200.417	27.554
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Measured			4247.86	5941.88	1694.02
	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	Ranked	Divided	0	11364	12941	1.13877
	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	Rooted	Subtracted		9.13761	12.1722	3.03459
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Measured	Divided	1	23693.7	18263	1.29736
	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Ranked			227.199	192.715	1.17894
	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	Rooted	Subtracted		55.6161	66.7332	11.1171
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Squared		0	6777.96	6288.98	488.98
	serpin b11. [swissprot;acc:q96p15]	Rooted	Divided		6.48074	7.48331	1.1547
	t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227]	Ranked	Subtracted		12715.9	11333.2	1382.7
	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	Measured	Divided		112.666	141.702	1.25772
171	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	Ranked	Subtracted		9875.43	11256.8	1381.37
	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]	Measured			594	402	192
	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812]	Squared	Divided	1	96602.7	69211.2	1.39577
	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]	Rooted		0	6.48074	7.48331	1.1547
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Measured	Subtracted	1	4117.67	5801.04	1683.37
	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	Rooted		0	30.7397	27.7265	3.0132
	germ cell-less. [refseq;acc:nm_022471]	Squared			3567.33	3084.18	483.15
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Rooted	Divided	1	61.6639	71.7355	1.16333
	lamin b2. [swissprot;acc:q03252]	Ranked		0	12135.4	13802	1.13733

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.