MK5 Microarray Data

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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Value Type	Gene	Rank	Interaction Map	green	description	Filtered	Network Comparison Type	network_comparison	red

Results: HTML CSV LaTeX

Showing element 782 to 831 of 3228 in total

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

Rank	green	description	network_comparison	red
782	235.131	translin. [swissprot;acc:q15631]	1.04789	224.385
783		translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
784		polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710]
785	233.508	neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863]	1.04685	244.447
786		rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555]
787		down-regulated in metastasis. [refseq;acc:nm_014503]
788	132.538	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	1.04653	138.705
789	234.511	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865]	1.04578	224.244
790		40s ribosomal protein s21. [swissprot;acc:p35265]
791		cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453]
792		maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]
793		bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595]
794		plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120]
795		serpin b11. [swissprot;acc:q96p15]
796		placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237]
797		cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
798		leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740]
799	212.404	sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900]	1.04501	221.965
800		nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307]
801	214.894	beta-catenin (pro2286). [swissprot;acc:p35222]	1.04445	224.445
802	221.785	testis-specific protein tex28. [swissprot;acc:o15482]	1.04425	212.386
803		similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61]
804		a kindred of iglon. [refseq;acc:nm_173808]
805		ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1]
806		inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370]
807		palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897]
808		beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115]
809		syntaxin 16 (syn16). [swissprot;acc:o14662]
810		27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
811		syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]
812		alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920]
813		adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9]
814		synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721]
815		syntaxin 1b. [swissprot;acc:q15531]
816		melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084]
817		dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593]
818	161.452	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6]	1.04422	168.592
819	238.668	dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954]	1.04421	228.563
820	231.501	mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399]	1.04413	221.716
821	231.453	u3 snornp protein 4 homolog. [refseq;acc:nm_033416]	1.0441	221.676
822	232.805	eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884]	1.04408	243.067
823	197.471	transcription factor iib. [refseq;acc:nm_013242]	1.04354	206.068
824		splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872]
825	197.614	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516]	1.04352	206.214
826	213.912	60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993]	1.04335	223.186
827	220.579	loh1cr12. [refseq;acc:nm_058169]	1.0431	230.087
828		unr protein. [swissprot;acc:o75534]
829	130.259	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]	1.04288	135.844
830	222.222	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562]	1.0428	231.734
831		hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.