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 1651 to 1700 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
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	
1680	CREBL1	cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [source:swissprot;acc:q99941]	216.899	213.889	1.01407	
1681	FAM50B	dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [source:refseq;acc:nm_012135]	216.899	213.889	1.01407	
1682	SRPK2	sfrs protein kinase 2 isoform b. [source:refseq;acc:nm_182691]	216.899	213.889	1.01407	
1683	ATF6	cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [source:swissprot;acc:p18850]	216.899	213.889	1.01407	
1684	SRPK1	sfrs protein kinase 1; sr protein kinase 1. [source:refseq;acc:nm_003137]	216.899	213.889	1.01407	
1685	FAM50A	xap-5 protein (hxc-26 protein). [source:swissprot;acc:q14320]	216.899	213.889	1.01407	
1686	OSGEPL1	putative sialoglycoprotease type 2. [source:refseq;acc:nm_022353]	220.75	217.704	1.01399	
1687	ATP5D	atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p30049]	215.345	212.386	1.01393	
1688	MORF4L1	transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [source:swissprot;acc:q9ubu8]	228.523	231.703	1.01392	
1689	DDX4	dead-box protein 4 (vasa homolog). [source:swissprot;acc:q9nqi0]	228.277	225.163	1.01383	
1690	RPS24	40s ribosomal protein s24 (s19). [source:swissprot;acc:p16632]	224.091	227.184	1.0138	
1691	EIF5B	translation initiation factor if-2. [source:swissprot;acc:o60841]	217.263	214.315	1.01376	
1692	RBM9	rna-binding protein 9 (rna binding motif protein 9) (hexaribonucleotide binding protein 2) (repressor of tamoxifen transcriptional activity). [source:swissprot;acc:o43251]	218.515	215.551	1.01375	
1693	IMPDH2	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [source:swissprot;acc:p12268]	218.937	215.971	1.01373	
1694	GMPS	gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [source:swissprot;acc:p49915]	218.937	215.971	1.01373	
1695	IMPDH1	inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [source:swissprot;acc:p20839]	218.937	215.971	1.01373	
1696	PABPC3	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [source:swissprot;acc:q9h361]	217.624	214.69	1.01367	
1697	KIN	hskin17 protein. [source:refseq;acc:nm_012311]	217.624	214.69	1.01367	
1698	CRAT	carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [source:swissprot;acc:p43155]	217.624	214.69	1.01367	
1699	PABPC4	polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [source:swissprot;acc:q13310]	217.624	214.69	1.01367	
1700	PABPC1	polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [source:swissprot;acc:p11940]	217.624	214.69	1.01367	

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/