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	network_comparison	red	green

Results: HTML CSV LaTeX

Showing element 1601 to 1650 of 3228 in total

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

Rank	description	network_comparison	red	green
1601	phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305]	1.01602	217.268	213.842
1602	phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871]	1.01599	217.334	213.914
1603	heat shock factor binding protein 1. [swissprot;acc:o75506]	1.01595	216.62	213.22
1604	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760]	1.01593	214.984	211.614
1605	hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317]	1.01592	217.322	213.916
1606	apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772]	1.0159	207.916	204.662
1607	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761]	1.01588	214.982	211.622
1608	ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349]	1.01581	208.106	204.867
1609	utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851]	1.0158	208.113	204.876
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]	1.01579	208.122	204.886
1611	p10-binding protein. [refseq;acc:nm_024491]	1.01577	221.313	217.877
1612	enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666]	1.0157	221.426	224.902
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]		182.378	185.241
1614	hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261]	1.0156	217.233	213.897
1615	dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282]		246.38	242.596
1616	n-acetylglutamate synthase. [refseq;acc:nm_153006]	1.01538	223.179	226.611
1617	serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896]	1.01537	221.045	217.699
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]	1.01527	227.768	231.246
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]	1.01521	228.611	225.185
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]	1.01518	230.643	227.194
1625	c18b11 homolog (44.9kd). [refseq;acc:nm_152260]	1.01515	217.446	214.2
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]	1.01511	218.789	215.533
1632	mitotic checkpoint protein bub3. [swissprot;acc:o43684]	1.01498	221.934	218.658
1633	zinc finger protein 207. [swissprot;acc:o43670]
1634	malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822]	1.01494	215.772	212.596
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]	1.01479	202.358	199.408
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]	1.01474	220.686	217.481
1639	yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906]	1.01464	194.516	197.364
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]	1.01457	218.167	215.034
1642	m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305]		260.269	256.531
1643	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	197.305
1644	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	1.01451	217.256	214.149
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]	1.01448	219.745	222.928
1649	neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730]	1.01445	219.062	215.942
1650	ring finger protein 44. [refseq;acc:nm_014901]

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.