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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2451 to 2500 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison	
1226	FDX1	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [source:swissprot;acc:p10109]	Subtracted	191.139	185.882	5.257	
1226	UBE2E4P	ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [source:refseq;acc:nm_006357]	Divided	166.846	170.989	1.02483	
1227	GCLM	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]	Subtracted	213.079	218.325	5.246	
1227	PYCR2	pyrroline 5-carboxylate reductase isoform. [source:refseq;acc:nm_013328]	Divided	172.365	168.219	1.02465	
1228	GCLC	glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [source:swissprot;acc:p48506]	Subtracted	213.079	218.325	5.246	
1228	GCLM	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]	Divided	213.079	218.325	1.02462	
1229		integral membrane protein cii-3b. [source:sptrembl;acc:o75609]	Subtracted	207.646	212.891	5.245	
1229	GCLC	glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [source:swissprot;acc:p48506]	Divided	213.079	218.325	1.02462	
1230	IL4I1	interleukin-4 induced protein 1 precursor (fig-1 protein). [source:swissprot;acc:q96rq9]	Divided	219.55	214.288	1.02456	
1230	SDHC	succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [source:swissprot;acc:q99643]	Subtracted	207.644	212.888	5.244	
1231	PGAM4	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [source:swissprot;acc:q8n0y7]	Divided	212.724	207.637	1.0245	
1231	SDHB	succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [source:swissprot;acc:p21912]	Subtracted	207.931	213.175	5.244	
1232		alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [source:swissprot;acc:p19652]	Subtracted	209.649	204.406	5.243	
1232	PYCR1	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [source:swissprot;acc:p32322]	Divided	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]	Divided	212.724	207.637	1.0245	
1233	SEPT1	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	Subtracted	142.077	136.846	5.231	
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). [source:swissprot;acc:p15259]	Divided	212.724	207.637	1.0245	
1234	UBB	ubiquitin. [source:swissprot;acc:p02248]	Subtracted	209.6	204.372	5.228	
1235		keratin associated protein 9-4; keratin associated protein 9.4. [source:refseq;acc:nm_033191]	Divided	219.356	224.723	1.02447	
1235	COPA	coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [source:swissprot;acc:p53621]	Subtracted	177.432	182.647	5.215	
1236		keratin associated protein 4-10; keratin associated protein 4.10. [source:refseq;acc:nm_033060]	Divided	219.354	224.699	1.02437	
1236	VBP1	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [source:swissprot;acc:q15765]	Subtracted	226.439	221.26	5.179	
1237		keratin associated protein 4-2; keratin associated protein 4.2. [source:refseq;acc:nm_033062]	Divided	219.354	224.699	1.02437	
1237	PFDN2	prefoldin subunit 2 (hspc231). [source:swissprot;acc:q9uhv9]	Subtracted	226.439	221.26	5.179	
1238		keratin associated protein 4.3 (fragment). [source:sptrembl;acc:q9byr4]	Divided	219.354	224.699	1.02437	
1238	UXT	uxt protein (ubiquitously expressed transcript protein) (hspc024). [source:swissprot;acc:q9ubk9]	Subtracted	226.439	221.26	5.179	
1239		keratin associated protein 2-4; keratin associated protein 2.4. [source:refseq;acc:nm_033184]	Divided	219.354	224.699	1.02437	
1239	STAT4	signal transducer and activator of transcription 4. [source:swissprot;acc:q14765]	Subtracted	222.573	227.751	5.178	
1240		keratin associated protein 4-14; keratin associated protein 4.14. [source:refseq;acc:nm_033059]	Divided	219.354	224.7	1.02437	
1240	STAT1	signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [source:swissprot;acc:p42224]	Subtracted	222.574	227.752	5.178	
1241		keratin associated protein 4.9 (fragment). [source:sptrembl;acc:q9byq8]	Divided	219.354	224.7	1.02437	
1241	STAT3	signal transducer and activator of transcription 3 (acute-phase response factor). [source:swissprot;acc:p40763]	Subtracted	222.573	227.75	5.177	
1242		keratin associated protein 4-12; keratin associated protein 4.12. [source:refseq;acc:nm_031854]	Divided	219.354	224.7	1.02437	
1242	RALGDS	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967]	Subtracted	162.055	156.884	5.171	
1243		keratin associated protein 1.5. [source:refseq;acc:nm_031957]	Divided	219.354	224.699	1.02437	
1243	STAT6	signal transducer and activator of transcription 6 (il-4 stat). [source:swissprot;acc:p42226]	Subtracted	222.569	227.739	5.17	
1244	STARD6	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [source:swissprot;acc:p59095]	Divided	219.354	224.7	1.02437	
1244	TPD52L1	tumor protein d53 (hd53) (d52-like 1). [source:swissprot;acc:q16890]	Subtracted	206.774	211.936	5.162	
1245	KRTAP5-8	keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [source:swissprot;acc:o75690]	Divided	219.354	224.699	1.02437	
1245	TPD52	tumor protein d52 (n8 protein). [source:swissprot;acc:p55327]	Subtracted	206.771	211.926	5.155	
1246		keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [source:swissprot;acc:p26371]	Divided	219.354	224.699	1.02437	
1246	SESN3	sestrin 3. [source:swissprot;acc:p58005]	Subtracted	218.368	213.219	5.149	
1247	SESN2	sestrin 2 (hi95). [source:swissprot;acc:p58004]	Subtracted	218.368	213.219	5.149	
1247	STARD5	star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [source:swissprot;acc:q9nsy2]	Divided	219.354	224.7	1.02437	
1248	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). [source:swissprot;acc:q02928]	Subtracted	218.368	213.22	5.148	
1248	KRTAP4-4	keratin associated protein 4.4. [source:refseq;acc:nm_032524]	Divided	219.354	224.699	1.02437	
1249		alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [source:swissprot;acc:q9nvd7]	Divided	219.354	224.7	1.02437	
1249	CYP4F3	cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:q08477]	Subtracted	218.368	213.22	5.148	
1250	CYP4F8	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [source:swissprot;acc:p98187]	Subtracted	218.368	213.22	5.148	
1250	LIMS1	pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [source:swissprot;acc:p48059]	Divided	219.354	224.7	1.02437	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/