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

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Showing element 2551 to 2600 of 3228 in total

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

red	Rank	green	description	network_comparison
6417.19	256	7859.51	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791]	1.22476
6417.31	257	7858.12	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	1.22452
6417.33	258	7857.93	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	1.22449
6417.81	259	7852.52	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	1.22355
6423.46	2434	6655.9	wd repeat domain 26. [refseq;acc:nm_025160]	1.03619
6435.02	1023	7044.65	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761]	1.09474
6435.94	1022	7045.75	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760]	1.09475
6436.19	1241	6980.13	26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200]	1.08451
6436.43	2529	6283	protein cgi-147. [swissprot;acc:q9y3e5]	1.02442
6436.73	1680	6882.16	methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898]	1.0692
6437.24	2071	6797.24	28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8]	1.05592
	2072		enhancer of rudimentary homolog. [swissprot;acc:q14259]
6437.49	1084	7029.22	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	1276	6969.67	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	1080	7031.73	secretory carrier-associated membrane protein 2. [swissprot;acc:o15127]	1.092
	1081		secretory carrier-associated membrane protein 3. [swissprot;acc:o14828]
6439.35	1082	7031.8	secretory carrier-associated membrane protein 1. [swissprot;acc:o15126]
6439.63	1076	7032.19	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	1077	7032.22	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	1321	6959.21	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	795	7154.13	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	1.11069
6441.17	794	7154.55	dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388]	1.11075
6441.56	1075	7034.86	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	1467	6932.39	p47 protein isoform a. [refseq;acc:nm_016143]	1.07572
6449.02	1623	6905.56	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	2534	6603.94	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	803	7167.96	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629]	1.11045
6455.66	802	7168.82	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	1.11047
6456.35	801	7169.75	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505]	1.1105
6469.44	2508	6634.31	lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766]	1.02548
6472.38	991	7092.65	transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595]	1.09583
6475.5	67	10307.5	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	2441	6695.58	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	2444	6695.67	adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2]	1.03358
6480.27	2347	6765.81	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	2259	6786.23	ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554]	1.04615

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.