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

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Showing element 982 to 1031 of 3228 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	red	green	network_comparison
982	adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3]	6654.42	7296.51	1.09649
983	vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836]
984	integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287]	6362.64	6976.1	1.09642
985	integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7]
986	integral membrane protein 2a (e25 protein). [swissprot;acc:o43736]
987	maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368]	6660.04	7301.81	1.09636
988	ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781]	6229.69	6829.58	1.0963
989	signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843]	11743.3	10712.3	1.09624
990	dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0]	5147.9	5641.25	1.09584
991	transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595]	6472.38	7092.65	1.09583
992	putative sialoglycoprotease type 2. [refseq;acc:nm_022353]	5393.37	5909.47	1.09569
993	arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815]	6499.89	7121.77	1.09568
994	interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9]	5800.95	6355.71	1.09563
995	annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995]	5778.65	6328.56	1.09516
996	methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5]	5110.6	5596.73	1.09512
997	nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838]	5144.74	5634	1.0951
998	transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269]
999	triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098]	5680.76	6220.45	1.095
1000	ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2]
1001	lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571]
1002	seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81]
1003	seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591]
1004	o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807]	5391.64	5903.72	1.09498
1005	annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073]	5780.34	6329.3	1.09497
1006	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936]	5707.73	6249.1	1.09485
1007	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794]
1008	single-minded homolog 1. [swissprot;acc:p81133]
1009	synapsin iii. [swissprot;acc:o14994]	5791.82	6340.86	1.0948
1010	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
1011	hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3]
1012	actin binding lim protein 2. [refseq;acc:nm_032432]
1013	hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571]
1014	synapsin ii. [swissprot;acc:q92777]
1015	mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]
1016	peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542]
1017	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259]
1018	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469]
1019	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
1020	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]
1021	synapsin i (brain protein 4.1). [swissprot;acc:p17600]
1022	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760]	6435.94	7045.75	1.09475
1023	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761]	6435.02	7044.65	1.09474
1024	cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238]	5706.5	6245.55	1.09446
1025	phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305]	5511.96	6031.95	1.09434
1026	phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871]	5509.89	6029.29	1.09427
1027	s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153]	6123.15	6700.05	1.09422
1028	nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274]	5704	6241.36	1.09421
1029	beta-catenin (pro2286). [swissprot;acc:p35222]	5635.26	6166.09	1.0942
1030	casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674]	5048.33	5523.85	1.09419
1031	membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792]	6136.99	6714.98	1.09418

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.