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 66312 in total

Filtered  : 1

Rank	description	Value Type	Network Comparison Type	Interaction Map	red	green	network_comparison
168	n-acetylglutamate synthase. [refseq;acc:nm_153006]	Measured	Subtracted	Low confidence	9395.91	10028.6	632.69
	nk6 transcription factor related, locus 2; nk homeobox family 6, b; glial and testis-specific homeobox protein; homeobox 6b. [refseq;acc:nm_177400]	Squared			64485.5	70068.3	5582.8
	proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591]	Ranked	Divided		216.796	205.073	1.05717
	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]		Subtracted		218.925	207.441	11.484
	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Squared	Divided	High confidence	173408	242989	1.40126
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Rooted	Subtracted		55.6161	66.7332	11.1171
	ring finger protein 20. [refseq;acc:nm_019592]	Squared	Divided	Low confidence	53551.4	48045.1	1.11461
	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	Rooted	Subtracted		84.7416	89.3094	4.5678
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]		Divided	High confidence	56.3709	65.8949	1.16895
169	60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914]	Ranked		Low confidence	216.79	205.07	1.05715
	apg3p; pc3-96 protein. [refseq;acc:nm_022488]			High confidence	82.5916	98.0548	1.18722
	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Rooted		Low confidence	72.4389	77.1711	1.06533
	cop-coated vesicle membrane protein p24 precursor (p24a). [swissprot;acc:q15363]	Squared	Subtracted		64485.5	70068.3	5582.8
	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653]	Rooted	Divided	High confidence	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
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Measured	Divided	Low confidence	12375.5	11435.8	1.08217
	f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907]	Ranked	Subtracted		213.671	202.205	11.466
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Measured		High confidence	4245.52	5942.75	1697.23
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]		Divided		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
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Rooted			55.6161	66.7332	11.1171
	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]			Low confidence	69.4376	64.8818	4.5558
	rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175]	Squared	Divided		67930.9	60946.6	1.1146
	symplekin. [swissprot;acc:q92797]			High confidence	124118	88668.8	1.39979
	tho complex 3. [refseq;acc:nm_032361]	Measured	Subtracted	Low confidence	7401.51	8028.16	626.65
170	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]	Squared			54860.1	49344.1	5516
	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	Measured	Divided		6131.26	6633.65	1.08194
	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]	Squared	Subtracted	High confidence	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
	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857]	Squared			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
	inad-like protein isoform 3; pdz domain protein (drosophila inad-like); protein associated to tight junctions; pals1-associated tight junction protein; inactivation no after-potential d-like protein. [refseq;acc:nm_005799]	Squared	Divided	Low confidence	67882.7	60913.7	1.11441
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Measured		High confidence	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
	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	Rooted		Low confidence	70.7428	75.3259	1.06479
	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]		Subtracted	High confidence	55.6161	66.7332	11.1171
	protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480]	Measured		Low confidence	8973.23	9597.94	624.71
	proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332]	Ranked	Divided		216.783	205.066	1.05714
	striatin. [swissprot;acc:o43815]	Rooted	Subtracted		66.4354	70.987	4.5516
	vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754]	Ranked			202.698	191.393	11.305
171	bet3 homolog. [swissprot;acc:o43617]	Measured			8749.42	9372.33	622.91
	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812]	Squared	Divided	High confidence	96602.7	69211.2	1.39577
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Rooted	Subtracted	Low confidence	98.0366	93.4864	4.5502
	defender against cell death 1 (dad-1). [swissprot;acc:p46966]	Ranked			197.99	186.913	11.077
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Measured		High confidence	4117.67	5801.04	1683.37
	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Ranked	Divided	Low confidence	219.889	208.064	1.05683
	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	Rooted			96.9641	103.242	1.06474
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]			High confidence	61.6639	71.7355	1.16333
	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]	Measured			23693.7	18263	1.29736

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.