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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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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 1630 to 1679 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison	
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	
1651	PIK3R1	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	RNF38	ring finger protein 38. [source:refseq;acc:nm_022781]	219.062	215.942	1.01445	
1653	PIK3R3	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	SCAP	sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [source:swissprot;acc:q12770]	219.062	215.942	1.01445	
1655	ATP5B	atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p06576]	219.062	215.942	1.01445	
1656	PIK3R2	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	NUDT21	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	ATP5A1	atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p25705]	217.925	214.826	1.01443	
1659	MRPS18A	28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [source:swissprot;acc:q9nvs2]	217.925	214.826	1.01443	
1660	EEA1	early endosome antigen 1, 162kd; early endosome-associated protein. [source:refseq;acc:nm_003566]	228.654	231.933	1.01434	
1661	ADSSL1	adenylosuccinate synthase-like 1. [source:refseq;acc:nm_152328]	204.437	201.551	1.01432	
1662	MORF4L2	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	TDO2	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	ADSS	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [source:swissprot;acc:p30520]	204.433	201.564	1.01423	
1666	TNPO2	karyopherin beta 2b, transportin; importin 3. [source:refseq;acc:nm_013433]	218.679	215.612	1.01422	
1667	CTSB	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [source:swissprot;acc:p07858]	214.898	211.898	1.01416	
1668		survival motor neuron protein (component of gems 1) (gemin1). [source:swissprot;acc:q16637]	228.496	231.729	1.01415	
1669		ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [source:swissprot;acc:p15154]	228.496	231.729	1.01415	
1670	RAC3	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [source:swissprot;acc:o14658]	228.496	231.729	1.01415	
1671	NUP54	nucleoporin 54kda; nucleoporin p54. [source:refseq;acc:nm_017426]	228.496	231.729	1.01415	
1672	RAC2	ras-related c3 botulinum toxin substrate 2 (p21-rac2) (small g protein) (gx). [source:swissprot;acc:p15153]	228.496	231.729	1.01415	
1673	MCM5	dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [source:swissprot;acc:p33992]	228.496	231.729	1.01415	
1674	SIP1	survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [source:swissprot;acc:o14893]	228.496	231.729	1.01415	
1675	DDX20	probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [source:swissprot;acc:q9uhi6]	228.496	231.729	1.01415	
1676	TNPO1	importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [source:swissprot;acc:q92973]	218.691	215.645	1.01413	
1677	GSTP1	glutathione s-transferase p (ec 2.5.1.18) (gst class-pi) (gstp1-1). [source:swissprot;acc:p09211]	218.654	221.732	1.01408	
1678	SRPK3	serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [source:swissprot;acc:q9upe1]	216.899	213.889	1.01407	
1679	GTPBP2	gtp binding protein 2. [source:refseq;acc:nm_019096]	216.899	213.889	1.01407	

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/