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

Results: HTML CSV LaTeX

Showing element 1600 to 1649 of 3228 in total

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

Rank	description	green	red	network_comparison
1600	adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [swissprot;acc:p21851]	225.675	222.103	1.01608
1601	phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305]	213.842	217.268	1.01602
1602	phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871]	213.914	217.334	1.01599
1603	heat shock factor binding protein 1. [swissprot;acc:o75506]	213.22	216.62	1.01595
1604	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760]	211.614	214.984	1.01593
1605	hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317]	213.916	217.322	1.01592
1606	apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772]	204.662	207.916	1.0159
1607	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761]	211.622	214.982	1.01588
1608	ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349]	204.867	208.106	1.01581
1609	utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851]	204.876	208.113	1.0158
1610	ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350]	204.886	208.122	1.01579
1611	p10-binding protein. [refseq;acc:nm_024491]	217.877	221.313	1.01577
1612	enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666]	224.902	221.426	1.0157
1613	hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410]	185.241	182.378
1614	hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261]	213.897	217.233	1.0156
1615	dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282]	242.596	246.38
1616	n-acetylglutamate synthase. [refseq;acc:nm_153006]	226.611	223.179	1.01538
1617	serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896]	217.699	221.045	1.01537
1618	transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [swissprot;acc:q15560]	231.246	227.768	1.01527
1619	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]
1620	transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403]	225.185	228.611	1.01521
1621	thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649]
1622	nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769]
1623	nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345]
1624	rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690]	227.194	230.643	1.01518
1625	c18b11 homolog (44.9kd). [refseq;acc:nm_152260]	214.2	217.446	1.01515
1626	z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24]
1627	pp1201 protein. [refseq;acc:nm_022152]
1628	lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]
1629	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]
1630	sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956]
1631	g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170]	215.533	218.789	1.01511
1632	mitotic checkpoint protein bub3. [swissprot;acc:o43684]	218.658	221.934	1.01498
1633	zinc finger protein 207. [swissprot;acc:o43670]
1634	malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822]	212.596	215.772	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]
1636	beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457]	199.408	202.358	1.01479
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	serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897]	217.481	220.686	1.01474
1639	yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906]	197.364	194.516	1.01464
1640	hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775]
1641	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]	215.034	218.167	1.01457
1642	m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305]	256.531	260.269
1643	myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572]	197.305	194.476	1.01455
1644	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	214.149	217.256	1.01451
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	hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597]	222.928	219.745	1.01448
1649	neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730]	215.942	219.062	1.01445

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.