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 1208 to 1257 of 3228 in total

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

Rank	description	red	green	network_comparison
1208	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	224.878	219.342	1.02524
1209	succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912]	207.931	213.175	1.02522
1210	kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139]	224.764	219.241	1.02519
1211	chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265]	214.364	219.759	1.02517
1212	kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9]
1213	conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746]
1214	kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]
1215	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]	218.268	212.916	1.02514
1216	retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338]	218.269	212.918	1.02513
1217	glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292]	211.959	217.258	1.025
1218	fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519]
1219	coactosin-like protein. [swissprot;acc:q14019]
1220	uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051]
1221	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]
1222	tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890]	206.774	211.936	1.02496
1223	tumor protein d52 (n8 protein). [swissprot;acc:p55327]	206.771	211.926	1.02493
1224	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	225.906	231.524	1.02487
1225	ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965]	166.846	170.989	1.02483
1226	ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357]
1227	pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328]	172.365	168.219	1.02465
1228	glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [swissprot;acc:p48507]	213.079	218.325	1.02462
1229	glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [swissprot;acc:p48506]
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

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.