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 1230 to 1279 of 3228 in total

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

Rank	description	red	green	network_comparison
1230	interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9]	219.55	214.288	1.02456
1231	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	212.724	207.637	1.0245
1232	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	172.543	168.417
1233	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]	212.724	207.637
1234	phosphoglycerate mutase 2 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme m) (pgam-m) (bpg-dependent pgam 2) (muscle-specific phosphoglycerate mutase). [swissprot;acc:p15259]
1235	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	219.356	224.723	1.02447
1236	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]	219.354	224.699	1.02437
1237	keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062]
1238	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]
1239	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]
1240	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]		224.7
1241	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]
1242	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]
1243	keratin associated protein 1.5. [refseq;acc:nm_031957]		224.699
1244	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]		224.7
1245	keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690]		224.699
1246	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]
1247	star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2]		224.7
1248	keratin associated protein 4.4. [refseq;acc:nm_032524]		224.699
1249	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]		224.7
1250	pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059]
1251	integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418]
1252	star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4]
1253	ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404]
1254	ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283]
1255	ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86]
1256	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]		224.699
1257	espin. [refseq;acc:nm_031475]		224.7
1258	cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635]
1259	pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832]
1260	lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980]
1261	d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917]
1262	keratin associated protein 9.2. [refseq;acc:nm_031961]	219.353	224.678	1.02428
1263	mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778]	171.231	167.177	1.02425
1264	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]
1265	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5]
1266	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1]
1267	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]
1268	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]
1269	nitrogen fixation cluster-like. [refseq;acc:nm_014301]
1270	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8]
1271	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502]
1272	neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]
1273	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635]
1274	mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539]
1275	neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681]
1276	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297]
1277	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]
1278	sestrin 3. [swissprot;acc:p58005]	218.368	213.219	1.02415
1279	sestrin 2 (hi95). [swissprot;acc:p58004]

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.