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 794 to 843 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
794	dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [source:swissprot;acc:p11388]	6441.17	7154.55	1.11075	
795	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [source:swissprot;acc:q02880]	6441.14	7154.13	1.11069	
796	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	6834.54	7590.49	1.11061	
797	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [source:swissprot;acc:q14974]	6834.54	7590.49	1.11061	
798	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [source:swissprot;acc:o60907]	6834.54	7590.49	1.11061	
799	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	6834.54	7590.49	1.11061	
800	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [source:swissprot;acc:q15406]	6075.55	6746.92	1.1105	
801	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [source:swissprot;acc:o00505]	6456.35	7169.75	1.1105	
802	target of egr1, member 1 (nuclear); target of egr1, member 1. [source:refseq;acc:nm_025077]	6455.66	7168.82	1.11047	
803	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [source:swissprot;acc:o00629]	6455.02	7167.96	1.11045	
804	nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [source:swissprot;acc:q9y6m9]	6770.78	7517.97	1.11036	
805	60s ribosomal protein l39. [source:swissprot;acc:p02404]	4708.61	5226.71	1.11003	
806	60s ribosomal protein l18a. [source:swissprot;acc:q02543]	4708.61	5226.71	1.11003	
807	40s ribosomal protein s19. [source:swissprot;acc:p39019]	4708.61	5226.71	1.11003	
808	60s ribosomal protein l31. [source:swissprot;acc:p12947]	4708.61	5226.71	1.11003	
809	wd-repeat protein 3. [source:swissprot;acc:q9unx4]	4039.81	4484.22	1.11001	
810	jm1 protein. [source:refseq;acc:nm_014008]	5794.8	6427.79	1.10923	
811	atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p30049]	6000.07	6655.11	1.10917	
812	target of myb protein 1. [source:swissprot;acc:o60784]	5640.79	6255.85	1.10904	
813	huntingtin-associated protein-interacting protein (duo protein). [source:swissprot;acc:o60229]	5641.11	6255.99	1.109	
814	triple functional domain protein (ptprf interacting protein). [source:swissprot;acc:o75962]	5641.12	6255.99	1.109	
815	midasin (midas-containing protein). [source:swissprot;acc:q9nu22]	4483.08	4971.62	1.10897	
816	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [source:refseq;acc:nm_144678]	5641.53	6256.17	1.10895	
817	ornithine decarboxylase (ec 4.1.1.17) (odc). [source:swissprot;acc:p11926]	6811.2	7547.35	1.10808	
818	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [source:refseq;acc:nm_005763]	6807.78	7543.28	1.10804	
819	ornithine decarboxylase antizyme inhibitor. [source:swissprot;acc:o14977]	6805.45	7540.5	1.10801	
820	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [source:swissprot;acc:q96a70]	6805.86	7540.99	1.10801	
821	trna isopentenylpyrophosphate transferase. [source:refseq;acc:nm_017646]	6257.99	6932.95	1.10786	
822	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [source:swissprot;acc:q08999]	6311.6	6989.33	1.10738	
823	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [source:swissprot;acc:p28749]	6311.83	6989.6	1.10738	
824	atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p36542]	5657.53	6263.02	1.10702	
825	atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [source:swissprot;acc:p48047]	5657.53	6263.02	1.10702	
826	exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [source:refseq;acc:nm_003400]	5195.58	5750.34	1.10678	
827	transcription factor smif; decapping enzyme hdcp1a. [source:refseq;acc:nm_018403]	5172.07	5723.22	1.10656	
828	puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [source:swissprot;acc:p55786]	5745.61	6354.75	1.10602	
829	leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [source:swissprot;acc:p09960]	5745.61	6354.75	1.10602	
830	dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [source:swissprot;acc:q02127]	5745.61	6354.75	1.10602	
831	t-cell activation wd repeat protein. [source:refseq;acc:nm_139281]	4062.03	4492.48	1.10597	
832	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [source:swissprot;acc:p25388]	4489.72	4965.35	1.10594	
833	zuotin related factor-1 (m-phase phosphoprotein 11). [source:swissprot;acc:q99543]	4489.72	4965.35	1.10594	
834	atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p25705]	5623.18	6218.77	1.10592	
835	28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [source:swissprot;acc:q9nvs2]	5623.18	6218.77	1.10592	
836	atp-dependent rna helicase rok1; atp-dependent rna helicase. [source:refseq;acc:nm_007010]	4049	4477.43	1.10581	
837	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [source:refseq;acc:nm_032830]	4063.64	4492.98	1.10565	
838	pbk1 protein. [source:sptrembl;acc:o76021]	4064.23	4493.36	1.10559	
839	arginyl-trna synthetase-like; arginine-trna ligase. [source:refseq;acc:nm_020320]	7093.86	7842.67	1.10556	
840	poly (adp-ribose) glycohydrolase. [source:refseq;acc:nm_003631]	5786.67	6395.78	1.10526	
841	mto1 protein homolog (cgi-02). [source:swissprot;acc:q9y2z2]	5786.67	6395.78	1.10526	
842	loh1cr12. [source:refseq;acc:nm_058169]	5195.48	5741.63	1.10512	
843	unr protein. [source:swissprot;acc:o75534]	5195.48	5741.63	1.10512	

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/