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 description Network Comparison Type Value Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 777 to 826 of 3228 in total 
Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	red	network_comparison	green	
777	histone deacetylase 1 (hd1). [source:swissprot;acc:q13547]	225.989	1.04853	215.53	
778	sorting nexin 6 (traf4-associated factor 2). [source:swissprot;acc:q9unh7]	209.191	1.04848	219.332	
779	deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [source:swissprot;acc:p32321]	230.516	1.04826	241.641	
780	dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [source:swissprot;acc:p41584]	232.762	1.04799	243.933	
781	ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [source:refseq;acc:nm_016183]	245.84	1.04798	257.636	
782	translin. [source:swissprot;acc:q15631]	224.385	1.04789	235.131	
783	translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	224.385	1.04789	235.131	
784	polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [source:refseq;acc:nm_005710]	224.385	1.04789	235.131	
785	neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [source:refseq;acc:nm_005863]	244.447	1.04685	233.508	
786	rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [source:refseq;acc:nm_019555]	244.447	1.04685	233.508	
787	down-regulated in metastasis. [source:refseq;acc:nm_014503]	244.447	1.04685	233.508	
788	hira-interacting protein 5 (cgi-33). [source:swissprot;acc:q9ums0]	138.705	1.04653	132.538	
789	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [source:swissprot;acc:p08865]	224.244	1.04578	234.511	
790	40s ribosomal protein s21. [source:swissprot;acc:p35265]	224.244	1.04578	234.511	
791	cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [source:swissprot;acc:p50453]	224.244	1.04578	234.511	
792	maspin precursor (protease inhibitor 5). [source:swissprot;acc:p36952]	224.244	1.04578	234.511	
793	bomapin (protease inhibitor 10) (serpin b10). [source:swissprot;acc:p48595]	224.244	1.04578	234.511	
794	plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [source:swissprot;acc:p05120]	224.244	1.04578	234.511	
795	serpin b11. [source:swissprot;acc:q96p15]	224.244	1.04578	234.511	
796	placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [source:swissprot;acc:p35237]	224.244	1.04578	234.511	
797	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [source:swissprot;acc:p50452]	224.244	1.04578	234.511	
798	leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [source:swissprot;acc:p30740]	224.244	1.04578	234.511	
799	sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [source:refseq;acc:nm_003900]	221.965	1.04501	212.404	
800	nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [source:swissprot;acc:p22307]	221.965	1.04501	212.404	
801	beta-catenin (pro2286). [source:swissprot;acc:p35222]	224.445	1.04445	214.894	
802	testis-specific protein tex28. [source:swissprot;acc:o15482]	212.386	1.04425	221.785	
803	similar to nuclear protein e3-3 orf1. [source:sptrembl;acc:q9bu61]	212.386	1.04425	221.785	
804	a kindred of iglon. [source:refseq;acc:nm_173808]	212.386	1.04425	221.785	
805	ankyrin-repeat family a protein 2 (rfxank-like 2). [source:swissprot;acc:q9h9e1]	212.386	1.04425	221.785	
806	inflammation-related g protein-coupled receptor ex33. [source:refseq;acc:nm_020370]	212.386	1.04425	221.785	
807	palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [source:swissprot;acc:p50897]	212.386	1.04425	221.785	
808	beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [source:swissprot;acc:q9h115]	212.386	1.04425	221.785	
809	syntaxin 16 (syn16). [source:swissprot;acc:o14662]	212.386	1.04425	221.785	
810	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [source:swissprot;acc:o14653]	212.386	1.04425	221.785	
811	syntaxin 1a (neuron-specific antigen hpc-1). [source:swissprot;acc:q16623]	212.386	1.04425	221.785	
812	alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [source:swissprot;acc:p54920]	212.386	1.04425	221.785	
813	adipocyte plasma membrane-associated protein (bscv protein). [source:swissprot;acc:q9hdc9]	212.386	1.04425	221.785	
814	synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [source:swissprot;acc:o95721]	212.386	1.04425	221.785	
815	syntaxin 1b. [source:swissprot;acc:q15531]	212.386	1.04425	221.785	
816	melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [source:swissprot;acc:q13084]	212.386	1.04425	221.785	
817	dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [source:swissprot;acc:o14593]	212.386	1.04425	221.785	
818	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [source:swissprot;acc:q9nzl6]	168.592	1.04422	161.452	
819	dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [source:swissprot;acc:p36954]	228.563	1.04421	238.668	
820	mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [source:swissprot;acc:q9y399]	221.716	1.04413	231.501	
821	u3 snornp protein 4 homolog. [source:refseq;acc:nm_033416]	221.676	1.0441	231.453	
822	eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [source:swissprot;acc:p55884]	243.067	1.04408	232.805	
823	transcription factor iib. [source:refseq;acc:nm_013242]	206.068	1.04354	197.471	
824	splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [source:swissprot;acc:q12872]	206.068	1.04354	197.471	
825	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [source:swissprot;acc:o43516]	206.214	1.04352	197.614	
826	60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [source:swissprot;acc:q92993]	223.186	1.04335	213.912	

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/