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

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Showing element 1844 to 1893 of 25824 in total

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

Rank	red	description	green	network_comparison
1844	3591.95	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252]	3375.34	1.06417
1845		nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]
1846		cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]
1847	6215.55	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104]	6613.46	1.06402
1848	5746.06	heat shock protein hsp 90-alpha (hsp 86). [swissprot;acc:p07900]	6113.79	1.064
1849	6267.93	arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540]	6668.72	1.06394
1850	6158.6	protein kinase c binding protein 1 (rack7) (cutaneous t-cell lymphoma associated antigen se14-3) (ctcl tumor antigen se14-3) (zinc finger mynd domain containing protein 8). [swissprot;acc:q9ulu4]	6551.94	1.06387
1851	6156.28	adenovirus 5 e1a-binding protein (bs69 protein). [swissprot;acc:q15326]	6549.03	1.0638
1852	6271.17	arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089]	6670.97	1.06375
1853	6076.65	keratin associated protein 9.2. [refseq;acc:nm_031961]	6463.64	1.06368
1854	6076.66	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]	6463.14	1.0636
1855		keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062]
1856		keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]
1857		keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	6463.15
1858		keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]	6463.13
1859		keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]
1860		keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]
1861		keratin associated protein 1.5. [refseq;acc:nm_031957]	6463.14
1862		star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	6463.13
1863		keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690]	6463.14
1864		keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]
1865		star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2]	6463.12
1866		keratin associated protein 4.4. [refseq;acc:nm_032524]	6463.14
1867		alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	6463.12
1868		pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059]
1869		integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418]
1870		star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4]	6463.13
1871		ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404]	6463.12
1872		ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283]
1873	3618.46	40s ribosomal protein s11. [swissprot;acc:p04643]	3402.09
1874	6076.66	ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86]	6463.12
1875		keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	6463.14
1876		espin. [refseq;acc:nm_031475]	6463.12
1877		cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635]
1878		pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832]
1879		lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980]
1880		d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917]
1881	6076.68	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	6462.56	1.0635
1882	5490.24	eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091]	5838.67	1.06346
1883	5826	26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]	6195.48	1.06342
1884		adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186]
1885		ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5]
1886		rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763]
1887	5438.6	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	5783.11	1.06335
1888		bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885]
1889	5438.68	testis-specific bromodomain protein. [refseq;acc:nm_001726]	5783.2
1890	5438.6	nag14 protein. [refseq;acc:nm_022143]	5783.11
1891	5438.18	bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059]	5782.62	1.06334
1892	5438.52	bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440]	5783.01
1893	6830.4	acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510]	7261.98	1.06319

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.