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

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

Results: HTML CSV LaTeX

Showing element 901 to 950 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

description	Rank	Network Comparison Type	red	green	network_comparison
bup protein. [refseq;acc:nm_012071]	2911	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
bystin. [swissprot;acc:q13895]	1050		239.505	233.185	6.32
	1149	Divided			1.0271
c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586]	1718	Subtracted	228.932	231.732	2.8
	1766	Divided			1.01223
c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [swissprot;acc:q9upt6]	2464	Subtracted	218.644	217.991	0.653
	2473	Divided			1.003
c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363]	1554		196.215	193.018	1.01656
	1628	Subtracted			3.197
c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545]	1558	Divided	196.171	192.977	1.01655
	1633	Subtracted			3.194
c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]	844	Divided	178.033	170.82	1.04223
	953	Subtracted			7.213
c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319]	2465		218.219	217.571	0.648
	2475	Divided			1.00298
c18b11 homolog (44.9kd). [refseq;acc:nm_152260]	1610	Subtracted	217.446	214.2	3.246
	1625	Divided			1.01515
c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0]	1506		212.103	208.339	1.01807
	1520	Subtracted			3.764
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	242		241.892	265.959	24.067
	321	Divided			1.09949
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	260		219.421	196.978	1.11394
	293	Subtracted			22.443
ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]	2577	Divided	192.625	192.922	1.00154
	2626	Subtracted			0.297
caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844]	1394		226.532	222.117	4.415
	1448	Divided			1.01988
cab2. [refseq;acc:nm_033419]	750	Subtracted	210.946	221.225	10.279
	769	Divided			1.04873
cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708]	1818	Subtracted	212.884	215.323	2.439
	1829	Divided			1.01146
cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517]	1506	Subtracted	219.306	223.179	3.873
	1526	Divided			1.01766
calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805]	1306	Subtracted	218.508	213.648	4.86
	1330	Divided			1.02275
calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206]	1305	Subtracted	218.509	213.649	4.86
	1328	Divided			1.02275
calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8]	1307	Subtracted			4.86
	1331	Divided			1.02275
calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746]	2494		194.527	195.08	1.00284
	2505	Subtracted			0.553
calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0]	2497	Divided			1.00284
	2508	Subtracted			0.553
calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]	940	Divided	212.442	205.088	1.03586
		Subtracted			7.354
calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194]	1082		209.052	203.183	5.869
	1100	Divided			1.02889
calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [swissprot;acc:q9uqm7]	2148	Subtracted	215.925	214.481	1.444
	2172	Divided			1.00673

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.