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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Value Type	Interaction Map	Gene	Rank	green	Filtered	description	Network Comparison Type	network_comparison	red

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Showing element 1630 to 1679 of 3228 in total

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

Rank	green	description	network_comparison	red
1630	214.2	sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956]	1.01515	217.446
1631	215.533	g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170]	1.01511	218.789
1632	218.658	mitotic checkpoint protein bub3. [swissprot;acc:o43684]	1.01498	221.934
1633		zinc finger protein 207. [swissprot;acc:o43670]
1634	212.596	malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822]	1.01494	215.772
1635		itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483]
1636	199.408	beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457]	1.01479	202.358
1637		26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210]
1638	217.481	serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897]	1.01474	220.686
1639	197.364	yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906]	1.01464	194.516
1640		hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775]
1641	215.034	proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [swissprot;acc:p28070]	1.01457	218.167
1642	256.531	m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305]		260.269
1643	197.305	myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572]	1.01455	194.476
1644	214.149	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	1.01451	217.256
1645		prefoldin subunit 1. [swissprot;acc:o60925]
1646		secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138]
1647		choline dehydrogenase. [refseq;acc:nm_018397]
1648	222.928	hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597]	1.01448	219.745
1649	215.942	neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730]	1.01445	219.062
1650		ring finger protein 44. [refseq;acc:nm_014901]
1651		phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986]
1652		ring finger protein 38. [refseq;acc:nm_022781]
1653		phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569]
1654		sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770]
1655		atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576]
1656		phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459]
1657	216.195	cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006]	1.01443	219.314
1658	214.826	atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705]		217.925
1659		28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2]
1660	231.933	early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566]	1.01434	228.654
1661	201.551	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	1.01432	204.437
1662	231.747	transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014]	1.01431	228.477
1663	215.26	tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775]	1.01429	218.335
1664	231.74	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]	1.01425	228.484
1665	201.564	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520]	1.01423	204.433
1666	215.612	karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433]	1.01422	218.679
1667	211.898	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]	1.01416	214.898
1668	231.729	survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]	1.01415	228.496
1669		ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]
1670		ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]
1671		nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426]
1672		ras-related c3 botulinum toxin substrate 2 (p21-rac2) (small g protein) (gx). [swissprot;acc:p15153]
1673		dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [swissprot;acc:p33992]
1674		survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [swissprot;acc:o14893]
1675		probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [swissprot;acc:q9uhi6]
1676	215.645	importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973]	1.01413	218.691
1677	221.732	glutathione s-transferase p (ec 2.5.1.18) (gst class-pi) (gstp1-1). [swissprot;acc:p09211]	1.01408	218.654
1678	213.889	serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1]	1.01407	216.899
1679		gtp binding protein 2. [refseq;acc:nm_019096]

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.