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

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Showing element 1233 to 1282 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison
1233	no value	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	1.0245
1234	PGAM2	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	no value	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	STARD6	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]		224.7
1245	KRTAP5-8	keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690]		224.699
1246	no value	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]
1247	STARD5	star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2]		224.7
1248	KRTAP4-4	keratin associated protein 4.4. [refseq;acc:nm_032524]		224.699
1249	no value	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]		224.7
1250	LIMS1	pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059]
1251	ILK	integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418]
1252	STARD4	star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4]
1253	RSU1	ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404]
1254	G3BP1	ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283]
1255	G3BP2	ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86]
1256	no value	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]		224.699
1257	ESPNP	espin. [refseq;acc:nm_031475]		224.7
1258	CYP2D6	cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635]
1259	PLEKHC1	pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832]
1260	LIMS2	lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980]
1261	DRD4	d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917]
1262	KRTAP9-8	keratin associated protein 9.2. [refseq;acc:nm_031961]	219.353	224.678	1.02428
1263	MAPK11	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	SPHK1	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]
1265	DPAGT1	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	DLC1	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	MAPKAPK2	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]
1268	CHRNA6	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]
1269	ISCU	nitrogen fixation cluster-like. [refseq;acc:nm_014301]
1270	STARD13	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8]
1271	STARD8	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502]
1272	CHRNA2	neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]
1273	MAPKAPK3	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635]
1274	MAPK14	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	CHRNA4	neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681]
1276	CHRNA3	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297]
1277	SPHK2	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]
1278	SESN3	sestrin 3. [swissprot;acc:p58005]	218.368	213.219	1.02415
1279	SESN2	sestrin 2 (hi95). [swissprot;acc:p58004]
1280	CYP4A11	cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928]		213.22	1.02414
1281	CYP4F3	cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477]
1282	CYP4F8	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]

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
- Hugo is the HGNC identifier if it exists
- 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.