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	Hugo	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 1630 to 1679 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison
1630	SREBF1	sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956]	217.446	214.2	1.01515
1631	GSPT1	g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170]	218.789	215.533	1.01511
1632	BUB3	mitotic checkpoint protein bub3. [swissprot;acc:o43684]	221.934	218.658	1.01498
1633	ZNF207	zinc finger protein 207. [swissprot;acc:o43670]
1634	MLYCD	malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822]	215.772	212.596	1.01494
1635	ITCH	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	BECN1	beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457]	202.358	199.408	1.01479
1637	PSMC5	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	SHMT2	serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897]	220.686	217.481	1.01474
1639	VPS72	yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906]	194.516	197.364	1.01464
1640	HAGH	hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775]
1641	PSMB4	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]	218.167	215.034	1.01457
1642	CDC25B	m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305]	260.269	256.531
1643	PNKD	myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572]	194.476	197.305	1.01455
1644	no value	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	217.256	214.149	1.01451
1645	PFDN1	prefoldin subunit 1. [swissprot;acc:o60925]
1646	SMOC2	secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138]
1647	CHDH	choline dehydrogenase. [refseq;acc:nm_018397]
1648	no value	hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597]	219.745	222.928	1.01448
1649	PRSS12	neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730]	219.062	215.942	1.01445
1650	RNF44	ring finger protein 44. [refseq;acc:nm_014901]
1651	PIK3R1	phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986]
1652	RNF38	ring finger protein 38. [refseq;acc:nm_022781]
1653	PIK3R3	phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569]
1654	SCAP	sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770]
1655	ATP5B	atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576]
1656	PIK3R2	phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459]
1657	NUDT21	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]	219.314	216.195	1.01443
1658	ATP5A1	atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705]	217.925	214.826
1659	MRPS18A	28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2]
1660	EEA1	early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566]	228.654	231.933	1.01434
1661	ADSSL1	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	204.437	201.551	1.01432
1662	MORF4L2	transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014]	228.477	231.747	1.01431
1663	TDO2	tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775]	218.335	215.26	1.01429
1664	no value	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]	228.484	231.74	1.01425
1665	ADSS	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520]	204.433	201.564	1.01423
1666	TNPO2	karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433]	218.679	215.612	1.01422
1667	CTSB	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]	214.898	211.898	1.01416
1668	no value	survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]	228.496	231.729	1.01415
1669		ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]
1670	RAC3	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]
1671	NUP54	nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426]
1672	RAC2	ras-related c3 botulinum toxin substrate 2 (p21-rac2) (small g protein) (gx). [swissprot;acc:p15153]
1673	MCM5	dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [swissprot;acc:p33992]
1674	SIP1	survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [swissprot;acc:o14893]
1675	DDX20	probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [swissprot;acc:q9uhi6]
1676	TNPO1	importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973]	218.691	215.645	1.01413
1677	GSTP1	glutathione s-transferase p (ec 2.5.1.18) (gst class-pi) (gstp1-1). [swissprot;acc:p09211]	218.654	221.732	1.01408
1678	SRPK3	serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1]	216.899	213.889	1.01407
1679	GTPBP2	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
- 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.