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

Results: HTML CSV LaTeX

Showing element 1480 to 1529 of 3228 in total

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

Rank	description	red	green	network_comparison
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
1508	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119]
1509	alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024]	225.148	221.177	1.01795
1510	beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025]
1511	cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1]	213.268	209.509	1.01794
1512	surfeit locus protein 1. [swissprot;acc:q15526]
1513	cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376]
1514	protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887]
1515	dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868]	213.267	209.511	1.01793
1516	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]
1517	seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884]
1518	[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874]	213.259	209.524	1.01783
1519	cone-rod homeobox protein. [swissprot;acc:o43186]	244.331	240.061	1.01779
1520	homeobox protein otx1. [swissprot;acc:p32242]	244.367	240.098	1.01778
1521	homeobox protein otx2. [swissprot;acc:p32243]	244.478	240.212	1.01776
1522	mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949]	219.306	223.179	1.01766
1523	putative ankyrin-repeat containing protein. [refseq;acc:nm_025185]
1524	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]
1525	protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8]
1526	cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517]
1527	mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772]
1528	hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318]	217.785	214.021	1.01759
1529	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	216.762	213.031	1.01751

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.