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 1458 to 1507 of 3228 in total

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

Rank	description	red	green	network_comparison
1458	eh-domain containing protein 3. [swissprot;acc:q9nzn3]	207.024	211.086	1.01962
1459	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060]	192.336	188.637	1.01961
1460	thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669]	205.817	209.851	1.0196
1461	reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799]	207.019	211.077
1462	dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957]	205.817	209.851
1463	pnas-18. [sptrembl;acc:q9bzu3]	161.056	164.211	1.01959
1464	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	217.351	213.18	1.01957
1465	mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]
1466	reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298]	207.022	211.073
1467	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	228.513	232.983	1.01956
1468	dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442]	212.001	207.937	1.01954
1469	reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197]	207.013	211.05	1.0195
1470	glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897]	221.412	217.199	1.0194
1471	spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623]
1472	glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250]
1473	glutamyl trna synthetase. [sptrembl;acc:o14563]
1474	importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410]	218.582	214.427	1.01938
1475	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	181.882	178.438	1.0193
1476	ran-gtp binding protein (fragment). [sptrembl;acc:o60518]	218.591	214.457	1.01928
1477	transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595]	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). [swissprot;acc:q15815]	215.122	211.066
1479	maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5]	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. [refseq;acc:nm_007007]	218.664	214.55	1.01918
1481	cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661]	208.432	204.516	1.01915
1482	limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]	224.354	220.15	1.0191
1483	pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177]	198.927	202.726
1484	2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694]
1485	j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330]	207.877	203.989	1.01906
1486	human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]
1487	zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822]
1488	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]
1489	mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318]	213.251	209.264	1.01905
1490	protein cgi-147. [swissprot;acc:q9y3e5]	221.961	226.186	1.01903
1491	glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744]	217.704	221.839	1.01899
1492	opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982]	224.159	220.017	1.01883
1493	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]	204.146	207.988	1.01882
1494	pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559]	204.133	207.967	1.01878
1495	casein kinase i alpha s-like. [refseq;acc:nm_145203]	229.459	225.237	1.01874
1496	casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729]
1497	exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400]	224.476	220.363	1.01866
1498	neurotrimin precursor (hnt). [swissprot;acc:q9p121]	224.022	219.924	1.01863
1499	transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403]	224.509	220.411	1.01859
1500	cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129]	213.398	209.52	1.01851
1501	kinesin family member c3. [refseq;acc:nm_005550]	214.727	210.838	1.01845
1502	uridine kinase-like 1. [swissprot;acc:q9nwz5]	218.084	214.149	1.01838
1503	hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043]	242.181	237.834	1.01828
1504	m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307]	259.439	254.797	1.01822
1505	protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0]	216.158	212.316	1.0181
1506	c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0]	212.103	208.339	1.01807
1507	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118]	213.274	209.5	1.01801

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.