Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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
Results: HTML CSV LaTeX Showing element 1618 to 1667 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1618	transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [source:swissprot;acc:q15560]	227.768	231.246	1.01527	
1619	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [source:swissprot;acc:p23193]	227.768	231.246	1.01527	
1620	transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [source:swissprot;acc:q00403]	228.611	225.185	1.01521	
1621	thyroid receptor interacting protein 3 (trip-3) (fragment). [source:swissprot;acc:q15649]	228.611	225.185	1.01521	
1622	nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [source:swissprot;acc:p55769]	228.611	225.185	1.01521	
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. [source:refseq;acc:nm_012345]	228.611	225.185	1.01521	
1624	rrp5 protein homolog (programmed cell death protein 11). [source:swissprot;acc:q14690]	230.643	227.194	1.01518	
1625	c18b11 homolog (44.9kd). [source:refseq;acc:nm_152260]	217.446	214.2	1.01515	
1626	z-protein (protein cgi-119) (s1r protein). [source:swissprot;acc:q9hc24]	217.446	214.2	1.01515	
1627	pp1201 protein. [source:refseq;acc:nm_022152]	217.446	214.2	1.01515	
1628	lifeguard; kiaa0950 protein. [source:refseq;acc:nm_012306]	217.446	214.2	1.01515	
1629	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [source:swissprot;acc:q12772]	217.446	214.2	1.01515	
1630	sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [source:swissprot;acc:p36956]	217.446	214.2	1.01515	
1631	g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [source:swissprot;acc:p15170]	218.789	215.533	1.01511	
1632	mitotic checkpoint protein bub3. [source:swissprot;acc:o43684]	221.934	218.658	1.01498	
1633	zinc finger protein 207. [source:swissprot;acc:o43670]	221.934	218.658	1.01498	
1634	malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [source:swissprot;acc:o95822]	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. [source:refseq;acc:nm_031483]	215.772	212.596	1.01494	
1636	beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [source:swissprot;acc:q14457]	202.358	199.408	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). [source:swissprot;acc:p47210]	202.358	199.408	1.01479	
1638	serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [source:swissprot;acc:p34897]	220.686	217.481	1.01474	
1639	yl-1 protein (transcription factor-like 1). [source:swissprot;acc:q15906]	194.516	197.364	1.01464	
1640	hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [source:swissprot;acc:q16775]	194.516	197.364	1.01464	
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). [source:swissprot;acc:p28070]	218.167	215.034	1.01457	
1642	m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [source:swissprot;acc:p30305]	260.269	256.531	1.01457	
1643	myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [source:refseq;acc:nm_022572]	194.476	197.305	1.01455	
1644	secreted modular calcium-binding protein 1. [source:refseq;acc:nm_022137]	217.256	214.149	1.01451	
1645	prefoldin subunit 1. [source:swissprot;acc:o60925]	217.256	214.149	1.01451	
1646	secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [source:refseq;acc:nm_022138]	217.256	214.149	1.01451	
1647	choline dehydrogenase. [source:refseq;acc:nm_018397]	217.256	214.149	1.01451	
1648	hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [source:swissprot;acc:p46597]	219.745	222.928	1.01448	
1649	neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [source:swissprot;acc:p56730]	219.062	215.942	1.01445	
1650	ring finger protein 44. [source:refseq;acc:nm_014901]	219.062	215.942	1.01445	
1651	phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [source:swissprot;acc:p27986]	219.062	215.942	1.01445	
1652	ring finger protein 38. [source:refseq;acc:nm_022781]	219.062	215.942	1.01445	
1653	phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [source:swissprot;acc:q92569]	219.062	215.942	1.01445	
1654	sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [source:swissprot;acc:q12770]	219.062	215.942	1.01445	
1655	atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p06576]	219.062	215.942	1.01445	
1656	phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [source:swissprot;acc:o00459]	219.062	215.942	1.01445	
1657	cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [source:refseq;acc:nm_007006]	219.314	216.195	1.01443	
1658	atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p25705]	217.925	214.826	1.01443	
1659	28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [source:swissprot;acc:q9nvs2]	217.925	214.826	1.01443	
1660	early endosome antigen 1, 162kd; early endosome-associated protein. [source:refseq;acc:nm_003566]	228.654	231.933	1.01434	
1661	adenylosuccinate synthase-like 1. [source:refseq;acc:nm_152328]	204.437	201.551	1.01432	
1662	transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [source:swissprot;acc:q15014]	228.477	231.747	1.01431	
1663	tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [source:swissprot;acc:p48775]	218.335	215.26	1.01429	
1664	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [source:swissprot;acc:q9y690]	228.484	231.74	1.01425	
1665	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [source:swissprot;acc:p30520]	204.433	201.564	1.01423	
1666	karyopherin beta 2b, transportin; importin 3. [source:refseq;acc:nm_013433]	218.679	215.612	1.01422	
1667	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [source:swissprot;acc:p07858]	214.898	211.898	1.01416	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/