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 3258 to 3307 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
1629	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]	Divided	217.446	214.2	1.01515
1630	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]	Subtracted	196.192	192.996	3.196
	sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956]	Divided	217.446	214.2	1.01515
1631	g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170]		218.789	215.533	1.01511
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	Subtracted	196.192	192.996	3.196
1632	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]		196.191		3.195
	mitotic checkpoint protein bub3. [swissprot;acc:o43684]	Divided	221.934	218.658	1.01498
1633	c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545]	Subtracted	196.171	192.977	3.194
	zinc finger protein 207. [swissprot;acc:o43670]	Divided	221.934	218.658	1.01498
1634	hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597]	Subtracted	219.745	222.928	3.183
	malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822]	Divided	215.772	212.596	1.01494
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]
	transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8]	Subtracted	228.523	231.703	3.18
1636	beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457]	Divided	202.358	199.408	1.01479
	malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822]	Subtracted	215.772	212.596	3.176
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]	Divided	202.358	199.408	1.01479
	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]	Subtracted	215.772	212.596	3.176
1638	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]		160.381	163.554	3.173
	serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897]	Divided	220.686	217.481	1.01474
1639	pnas-18. [sptrembl;acc:q9bzu3]	Subtracted	161.056	164.211	3.155
	yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906]	Divided	194.516	197.364	1.01464
1640	hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775]
	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]	Subtracted	218.167	215.034	3.133
1641	neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730]		219.062	215.942	3.12
	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]	Divided	218.167	215.034	1.01457
1642	m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305]		260.269	256.531
	ring finger protein 44. [refseq;acc:nm_014901]	Subtracted	219.062	215.942	3.12
1643	myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572]	Divided	194.476	197.305	1.01455
	phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986]	Subtracted	219.062	215.942	3.12
1644	ring finger protein 38. [refseq;acc:nm_022781]
	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	Divided	217.256	214.149	1.01451
1645	phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569]	Subtracted	219.062	215.942	3.12
	prefoldin subunit 1. [swissprot;acc:o60925]	Divided	217.256	214.149	1.01451
1646	secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138]
	sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770]	Subtracted	219.062	215.942	3.12
1647	atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576]
	choline dehydrogenase. [refseq;acc:nm_018397]	Divided	217.256	214.149	1.01451
1648	hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597]		219.745	222.928	1.01448
	phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459]	Subtracted	219.062	215.942	3.12
1649	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	3.119
	neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730]	Divided	219.062	215.942	1.01445
1650	dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0]	Subtracted	228.277	225.163	3.114
	ring finger protein 44. [refseq;acc:nm_014901]	Divided	219.062	215.942	1.01445
1651	phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986]
	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	Subtracted	217.256	214.149	3.107
1652	prefoldin subunit 1. [swissprot;acc:o60925]
	ring finger protein 38. [refseq;acc:nm_022781]	Divided	219.062	215.942	1.01445
1653	phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569]
	secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138]	Subtracted	217.256	214.149	3.107
1654	choline dehydrogenase. [refseq;acc:nm_018397]

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.