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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
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	Hugo	description	red	green	network_comparison	
1601	PMM2	phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [source:swissprot;acc:o15305]	217.268	213.842	1.01602	
1602	PMM1	phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [source:swissprot;acc:q92871]	217.334	213.914	1.01599	
1603		heat shock factor binding protein 1. [source:swissprot;acc:o75506]	216.62	213.22	1.01595	
1604	CLK2	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [source:swissprot;acc:p49760]	214.984	211.614	1.01593	
1605	FOXA1	hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [source:swissprot;acc:p55317]	217.322	213.916	1.01592	
1606	APOA1BP	apolipoprotein a-i binding protein; apoa-i binding protein. [source:refseq;acc:nm_144772]	207.916	204.662	1.0159	
1607	CLK3	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [source:swissprot;acc:p49761]	214.982	211.622	1.01588	
1608	TMEM189	ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [source:refseq;acc:nm_003349]	208.106	204.867	1.01581	
1609	UGP2	utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [source:swissprot;acc:q16851]	208.113	204.876	1.0158	
1610	UBE2V2	ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [source:refseq;acc:nm_003350]	208.122	204.886	1.01579	
1611	CEP70	p10-binding protein. [source:refseq;acc:nm_024491]	221.313	217.877	1.01577	
1612		enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [source:refseq;acc:nm_014666]	221.426	224.902	1.0157	
1613	HTATIP2	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. [source:refseq;acc:nm_006410]	182.378	185.241	1.0157	
1614	FOXA2	hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [source:swissprot;acc:q9y261]	217.233	213.897	1.0156	
1615	POLE2	dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [source:swissprot;acc:p56282]	246.38	242.596	1.0156	
1616	NAGS	n-acetylglutamate synthase. [source:refseq;acc:nm_153006]	223.179	226.611	1.01538	
1617	SHMT1	serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [source:swissprot;acc:p34896]	221.045	217.699	1.01537	
1618	TCEA2	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	GTF2B	transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [source:swissprot;acc:q00403]	228.611	225.185	1.01521	
1621	ZNHIT3	thyroid receptor interacting protein 3 (trip-3) (fragment). [source:swissprot;acc:q15649]	228.611	225.185	1.01521	
1622	NHP2L1	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	NUFIP1	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	PDCD11	rrp5 protein homolog (programmed cell death protein 11). [source:swissprot;acc:q14690]	230.643	227.194	1.01518	
1625	RPUSD2	c18b11 homolog (44.9kd). [source:refseq;acc:nm_152260]	217.446	214.2	1.01515	
1626	TMBIM4	z-protein (protein cgi-119) (s1r protein). [source:swissprot;acc:q9hc24]	217.446	214.2	1.01515	
1627	TMBIM1	pp1201 protein. [source:refseq;acc:nm_022152]	217.446	214.2	1.01515	
1628	FAIM2	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	SREBF1	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	GSPT1	g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [source:swissprot;acc:p15170]	218.789	215.533	1.01511	
1632	BUB3	mitotic checkpoint protein bub3. [source:swissprot;acc:o43684]	221.934	218.658	1.01498	
1633	ZNF207	zinc finger protein 207. [source:swissprot;acc:o43670]	221.934	218.658	1.01498	
1634	MLYCD	malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [source: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. [source:refseq;acc:nm_031483]	215.772	212.596	1.01494	
1636	BECN1	beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [source: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). [source:swissprot;acc:p47210]	202.358	199.408	1.01479	
1638	SHMT2	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	VPS72	yl-1 protein (transcription factor-like 1). [source:swissprot;acc:q15906]	194.516	197.364	1.01464	
1640	HAGH	hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [source:swissprot;acc:q16775]	194.516	197.364	1.01464	
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). [source: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). [source:swissprot;acc:p30305]	260.269	256.531	1.01457	
1643	PNKD	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	PFDN1	prefoldin subunit 1. [source:swissprot;acc:o60925]	217.256	214.149	1.01451	
1646	SMOC2	secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [source:refseq;acc:nm_022138]	217.256	214.149	1.01451	
1647	CHDH	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	PRSS12	neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [source:swissprot;acc:p56730]	219.062	215.942	1.01445	
1650	RNF44	ring finger protein 44. [source:refseq;acc:nm_014901]	219.062	215.942	1.01445	

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