Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

Results: HTML CSV LaTeX

Showing element 1218 to 1267 of 3228 in total

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

Rank	description	red	green	network_comparison	
1218	fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [source:swissprot;acc:o00519]	211.959	217.258	1.025	
1219	coactosin-like protein. [source:swissprot;acc:q14019]	211.959	217.258	1.025	
1220	uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [source:swissprot;acc:p13051]	211.959	217.258	1.025	
1221	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [source:swissprot;acc:o75879]	211.959	217.258	1.025	
1222	tumor protein d53 (hd53) (d52-like 1). [source:swissprot;acc:q16890]	206.774	211.936	1.02496	
1223	tumor protein d52 (n8 protein). [source:swissprot;acc:p55327]	206.771	211.926	1.02493	
1224	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [source: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). [source:swissprot;acc:p51965]	166.846	170.989	1.02483	
1226	ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [source:refseq;acc:nm_006357]	166.846	170.989	1.02483	
1227	pyrroline 5-carboxylate reductase isoform. [source: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). [source: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). [source:swissprot;acc:p48506]	213.079	218.325	1.02462	
1230	interleukin-4 induced protein 1 precursor (fig-1 protein). [source: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). [source:swissprot;acc:q8n0y7]	212.724	207.637	1.0245	
1232	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [source:swissprot;acc:p32322]	172.543	168.417	1.0245	
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). [source:swissprot;acc:p18669]	212.724	207.637	1.0245	
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). [source:swissprot;acc:p15259]	212.724	207.637	1.0245	
1235	keratin associated protein 9-4; keratin associated protein 9.4. [source:refseq;acc:nm_033191]	219.356	224.723	1.02447	
1236	keratin associated protein 4-10; keratin associated protein 4.10. [source:refseq;acc:nm_033060]	219.354	224.699	1.02437	
1237	keratin associated protein 4-2; keratin associated protein 4.2. [source:refseq;acc:nm_033062]	219.354	224.699	1.02437	
1238	keratin associated protein 4.3 (fragment). [source:sptrembl;acc:q9byr4]	219.354	224.699	1.02437	
1239	keratin associated protein 2-4; keratin associated protein 2.4. [source:refseq;acc:nm_033184]	219.354	224.699	1.02437	
1240	keratin associated protein 4-14; keratin associated protein 4.14. [source:refseq;acc:nm_033059]	219.354	224.7	1.02437	
1241	keratin associated protein 4.9 (fragment). [source:sptrembl;acc:q9byq8]	219.354	224.7	1.02437	
1242	keratin associated protein 4-12; keratin associated protein 4.12. [source:refseq;acc:nm_031854]	219.354	224.7	1.02437	
1243	keratin associated protein 1.5. [source:refseq;acc:nm_031957]	219.354	224.699	1.02437	
1244	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [source:swissprot;acc:p59095]	219.354	224.7	1.02437	
1245	keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [source:swissprot;acc:o75690]	219.354	224.699	1.02437	
1246	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [source:swissprot;acc:p26371]	219.354	224.699	1.02437	
1247	star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [source:swissprot;acc:q9nsy2]	219.354	224.7	1.02437	
1248	keratin associated protein 4.4. [source:refseq;acc:nm_032524]	219.354	224.699	1.02437	
1249	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [source:swissprot;acc:q9nvd7]	219.354	224.7	1.02437	
1250	pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [source:swissprot;acc:p48059]	219.354	224.7	1.02437	
1251	integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [source:swissprot;acc:q13418]	219.354	224.7	1.02437	
1252	star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [source:swissprot;acc:q96dr4]	219.354	224.7	1.02437	
1253	ras suppressor protein 1 (rsu-1) (rsp-1). [source:swissprot;acc:q15404]	219.354	224.7	1.02437	
1254	ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [source:swissprot;acc:q13283]	219.354	224.7	1.02437	
1255	ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [source:swissprot;acc:q9un86]	219.354	224.7	1.02437	
1256	keratin associated protein 1-3; keratin associated protein 1.3. [source:refseq;acc:nm_030966]	219.354	224.699	1.02437	
1257	espin. [source:refseq;acc:nm_031475]	219.354	224.7	1.02437	
1258	cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [source:swissprot;acc:p10635]	219.354	224.7	1.02437	
1259	pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [source:refseq;acc:nm_006832]	219.354	224.7	1.02437	
1260	lim and senescent cell antigen-like domains 2; ilk-binding protein. [source:refseq;acc:nm_017980]	219.354	224.7	1.02437	
1261	d(4) dopamine receptor (d(2c) dopamine receptor). [source:swissprot;acc:p21917]	219.354	224.7	1.02437	
1262	keratin associated protein 9.2. [source: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). [source:swissprot;acc:p53778]	171.231	167.177	1.02425	
1264	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [source:swissprot;acc:q9nya1]	171.231	167.177	1.02425	
1265	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [source:swissprot;acc:q9h3h5]	171.231	167.177	1.02425	
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). [source:swissprot;acc:q96qb1]	171.231	167.177	1.02425	
1267	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [source:swissprot;acc:p49137]	171.231	167.177	1.02425	

Legend:
- Rank is the rank after comparing the two networks
- 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.

- http://analysis.yellowcouch.org/