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 1513 to 1562 of 3730 in total

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

Rank	description	red	green	network_comparison
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]	5791.82	6340.86	1.0948
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
1032	ran binding protein 11. [refseq;acc:nm_016338]	6138.91	6717.05
1033	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	6080.91	6653.52	1.09417
1034	s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266]	6152.88	6732.12	1.09414
1035	casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730]	5054.73	5530.23	1.09407
1036	fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467]	6077.65	6649.22	1.09404
1037	monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283]	6544.26	7159.43	1.094
1038	myb proto-oncogene protein (c-myb). [swissprot;acc:p10242]	5417.95	5924.41	1.09348
1039	myb-related protein b (b-myb). [swissprot;acc:p10244]	5418.92	5923.09	1.09304
1040	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	5421.93	5926.08	1.09298
1041	myb-related protein a (a-myb). [swissprot;acc:p10243]	5419.18	5922.84	1.09294
1042	similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2]	5887.52	6434.32	1.09287
1043	15 kda selenoprotein precursor. [swissprot;acc:o60613]	6344.41	6933.36	1.09283
1044	mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517]	4757.46	5198.91	1.09279
1045	immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197]	5364.32	5862.09
1046	skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9]	4757.46	5198.91
1047	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]
1048	tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289]
1049	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]
1050	neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1]
1051	homeobox protein dlx-2. [swissprot;acc:q07687]
1052	homeobox protein dlx-5. [swissprot;acc:p56178]
1053	fetal brain protein 239 (239fb). [swissprot;acc:q15777]
1054	homeobox protein dlx-3. [swissprot;acc:o60479]
1055	activated p21cdc42hs kinase. [refseq;acc:nm_005781]
1056	mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093]
1057	tata element modulatory factor (tmf). [swissprot;acc:p82094]	5412.23	5913.4	1.0926
1058	scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680]
1059	tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814]	5719.01	6248.6
1060	putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305]

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.