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 2913 to 2962 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1457	eh-domain containing protein 2. [source:swissprot;acc:q9nzn4]	Divided	207.024	211.086	1.01962	
1457	transformer-2 protein homolog (tra-2 alpha). [source:swissprot;acc:q13595]	Subtracted	215.328	211.267	4.061	
1458	eh-domain containing protein 1 (testilin) (hpast1). [source:swissprot;acc:q9h4m9]	Subtracted	207.024	211.085	4.061	
1458	eh-domain containing protein 3. [source:swissprot;acc:q9nzn3]	Divided	207.024	211.086	1.01962	
1459	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [source:swissprot;acc:p55060]	Divided	192.336	188.637	1.01961	
1459	reticulon 1 (neuroendocrine-specific protein). [source:swissprot;acc:q16799]	Subtracted	207.019	211.077	4.058	
1460	arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [source:swissprot;acc:q15815]	Subtracted	215.122	211.066	4.056	
1460	thyroid receptor interacting protein 12 (trip12). [source:swissprot;acc:q14669]	Divided	205.817	209.851	1.0196	
1461	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]	Subtracted	171.231	167.177	4.054	
1461	reticulon 1 (neuroendocrine-specific protein). [source:swissprot;acc:q16799]	Divided	207.019	211.077	1.0196	
1462	dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [source:swissprot;acc:p36957]	Divided	205.817	209.851	1.0196	
1462	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [source:swissprot;acc:q9nya1]	Subtracted	171.231	167.177	4.054	
1463	pnas-18. [source:sptrembl;acc:q9bzu3]	Divided	161.056	164.211	1.01959	
1463	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]	Subtracted	171.231	167.177	4.054	
1464	poly (adp-ribose) glycohydrolase. [source:refseq;acc:nm_003631]	Divided	217.351	213.18	1.01957	
1464	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]	Subtracted	171.231	167.177	4.054	
1465	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [source:swissprot;acc:p49137]	Subtracted	171.231	167.177	4.054	
1465	mto1 protein homolog (cgi-02). [source:swissprot;acc:q9y2z2]	Divided	217.351	213.18	1.01957	
1466	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [source:swissprot;acc:q15825]	Subtracted	171.231	167.177	4.054	
1466	reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [source:swissprot;acc:o75298]	Divided	207.022	211.073	1.01957	
1467	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [source:swissprot;acc:q14168]	Divided	228.513	232.983	1.01956	
1467	nitrogen fixation cluster-like. [source:refseq;acc:nm_014301]	Subtracted	171.231	167.177	4.054	
1468	dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [source:refseq;acc:nm_006442]	Divided	212.001	207.937	1.01954	
1468	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [source:swissprot;acc:q9y3m8]	Subtracted	171.231	167.177	4.054	
1469	reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [source:swissprot;acc:o95197]	Divided	207.013	211.05	1.0195	
1469	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [source:swissprot;acc:q92502]	Subtracted	171.231	167.177	4.054	
1470	glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [source:swissprot;acc:p47897]	Divided	221.412	217.199	1.0194	
1470	neuronal acetylcholine receptor protein, alpha-2 chain precursor. [source:swissprot;acc:q15822]	Subtracted	171.231	167.177	4.054	
1471	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [source:refseq;acc:nm_004635]	Subtracted	171.231	167.177	4.054	
1471	spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [source:swissprot;acc:p19623]	Divided	221.412	217.199	1.0194	
1472	glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [source:swissprot;acc:p41250]	Divided	221.412	217.199	1.0194	
1472	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). [source:swissprot;acc:q16539]	Subtracted	171.231	167.177	4.054	
1473	glutamyl trna synthetase. [source:sptrembl;acc:o14563]	Divided	221.412	217.199	1.0194	
1473	neuronal acetylcholine receptor protein, alpha-4 chain precursor. [source:swissprot;acc:p43681]	Subtracted	171.231	167.177	4.054	
1474	importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [source:swissprot;acc:o00410]	Divided	218.582	214.427	1.01938	
1474	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [source:swissprot;acc:p32297]	Subtracted	171.231	167.177	4.054	
1475	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [source:swissprot;acc:q16719]	Divided	181.882	178.438	1.0193	
1475	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [source:swissprot;acc:q9nra0]	Subtracted	171.231	167.177	4.054	
1476	ran-gtp binding protein (fragment). [source:sptrembl;acc:o60518]	Divided	218.591	214.457	1.01928	
1476	reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [source:swissprot;acc:o75298]	Subtracted	207.022	211.073	4.051	
1477	reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [source:swissprot;acc:o95197]	Subtracted	207.013	211.05	4.037	
1477	transformer-2 protein homolog (tra-2 alpha). [source:swissprot;acc:q13595]	Divided	215.328	211.267	1.01922	
1478	arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [source:swissprot;acc:q15815]	Divided	215.122	211.066	1.01922	
1478	thyroid receptor interacting protein 12 (trip12). [source:swissprot;acc:q14669]	Subtracted	205.817	209.851	4.034	
1479	dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [source:swissprot;acc:p36957]	Subtracted	205.817	209.851	4.034	
1479	maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [source:swissprot;acc:q9nzw5]	Divided	228.469	232.855	1.0192	
1480	cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [source:refseq;acc:nm_007007]	Divided	218.664	214.55	1.01918	
1480	mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [source:swissprot;acc:o43318]	Subtracted	213.251	209.264	3.987	
1481	alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [source:swissprot;acc:p42024]	Subtracted	225.148	221.177	3.971	
1481	cell division cycle protein 23; anaphase-promoting complex subunit 8. [source:refseq;acc:nm_004661]	Divided	208.432	204.516	1.01915	

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/