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

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Showing element 2563 to 2612 of 3228 in total

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

red	green	Rank	description	network_comparison
6437.49	7029.22	1084	phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674]	1.09192
6437.99	6969.67	1276	peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77]	1.08258
		1277	heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652]
		1278	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]
		1279	heat shock cognate 71 kda protein. [swissprot;acc:p11142]
6439.3	7031.73	1080	secretory carrier-associated membrane protein 2. [swissprot;acc:o15127]	1.092
		1081	secretory carrier-associated membrane protein 3. [swissprot;acc:o14828]
6439.35	7031.8	1082	secretory carrier-associated membrane protein 1. [swissprot;acc:o15126]
6439.63	7032.19	1076	solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4]	1.09202
		1078	solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2]
6439.66	7032.22	1077	solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9]
		1079	solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183]
6439.79	6959.21	1321	suppressor of var1, 3-like 1. [refseq;acc:nm_003171]	1.08066
		1322	bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933]
		1323	glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840]
		1324	glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841]
6441.14	7154.13	795	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	1.11069
6441.17	7154.55	794	dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388]	1.11075
6441.56	7034.86	1075	phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903]	1.09211
6444.4	6932.39	1467	p47 protein isoform a. [refseq;acc:nm_016143]	1.07572
6449.02	6905.56	1623	transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [swissprot;acc:p55072]	1.07079
6452.33	6603.94	2534	thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669]	1.0235
		2535	dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957]
6455.02	7167.96	803	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629]	1.11045
6455.66	7168.82	802	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	1.11047
6456.35	7169.75	801	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505]	1.1105
6469.44	6634.31	2508	lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766]	1.02548
6472.38	7092.65	991	transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595]	1.09583
6475.5	10307.5	67	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	1.59177
		68	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]
		69	spermatogenesis associated 6. [refseq;acc:nm_019073]
		70	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
6477.82	6695.58	2441	adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [swissprot;acc:p53677]	1.03362
6478.14	6695.67	2444	adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2]	1.03358
6480.27	6765.81	2347	ral guanine nucleotide exchange factor ralgps1a. [refseq;acc:nm_014636]	1.04406
		2348	ral-a exchange factor ralgps2. [refseq;acc:nm_152663]
		2350	stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861]
6486.84	6786.23	2259	ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554]	1.04615
		2261	38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]
6499.89	7121.77	993	arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815]	1.09568
6503.03	7282.5	680	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520]	1.11986
6503.1	7282.94	679	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	1.11992
6513.45	7161	914	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]	1.09942
6520.28	7119.28	1085	glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057]	1.09187
		1086	proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272]
6520.83	6946.75	1810	colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508]	1.06532
6522.94	7175.18	910	sipl protein. [refseq;acc:nm_018269]	1.09999
6522.96	7023.77	1440	peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381]	1.07678
6523.17	7019.44	1466	proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074]	1.07608
6527.56	6608.61	2637	protein kinase nyd-sp25. [refseq;acc:nm_033516]	1.01242

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.