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 975 to 1024 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
488	gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	Subtracted	82.5916	98.0548	15.4632	
488	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [source:refseq;acc:nm_005146]	Divided	225.026	209.798	1.07258	
489	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	Subtracted	82.5916	98.0548	15.4632	
489	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [source:swissprot;acc:o75688]	Divided	231.276	215.627	1.07257	
490	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [source:swissprot;acc:p05455]	Subtracted	242.531	227.136	15.395	
490	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [source:swissprot;acc:q14155]	Divided	220.183	236.015	1.0719	
491	metalloprotease 1; metalloprotease 1 (pitrilysin family). [source:refseq;acc:nm_014889]	Subtracted	150.959	166.351	15.392	
491	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [source:swissprot;acc:q9bze4]	Divided	251.83	234.951	1.07184	
492	beta-1,4 mannosyltransferase. [source:refseq;acc:nm_019109]	Subtracted	150.982	166.372	15.39	
492	serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [source:swissprot;acc:q13177]	Divided	220.171	235.979	1.0718	
493	conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [source:swissprot;acc:q9up83]	Divided	220.172	235.98	1.0718	
493	zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [source:refseq;acc:nm_014596]	Subtracted	236.751	252.038	15.287	
494	metaxin 2. [source:swissprot;acc:o75431]	Subtracted	219.537	234.793	15.256	
494	serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [source:swissprot;acc:q13153]	Divided	220.172	235.98	1.0718	
495	serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [source:swissprot;acc:o75914]	Divided	220.171	235.979	1.0718	
495	yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [source:refseq;acc:nm_014263]	Subtracted	222.146	237.393	15.247	
496	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [source:sptrembl;acc:q9h5a9]	Subtracted	235.18	250.419	15.239	
496	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [source:swissprot;acc:q9nq55]	Divided	250.938	234.134	1.07177	
497	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [source:swissprot;acc:q99848]	Divided	251.344	234.514	1.07177	
497	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [source:refseq;acc:nm_005146]	Subtracted	225.026	209.798	15.228	
498	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [source:swissprot;acc:q15052]	Divided	220.161	235.95	1.07172	
498	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [source:swissprot;acc:o43711]	Subtracted	237.28	252.492	15.212	
499	homeobox protein barh-like 1. [source:swissprot;acc:q9hbu1]	Subtracted	237.28	252.492	15.212	
499	triosephosphate isomerase (ec 5.3.1.1) (tim). [source:swissprot;acc:p00938]	Divided	231.496	248.048	1.0715	
500	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [source:refseq;acc:nm_001564]	Divided	224.662	240.673	1.07127	
500	opsin 4 (melanopsin). [source:swissprot;acc:q9uhm6]	Subtracted	237.28	252.492	15.212	
501	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [source:swissprot;acc:p08574]	Divided	238.704	255.68	1.07112	
501	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [source:swissprot;acc:o43763]	Subtracted	237.28	252.492	15.212	
502	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [source:swissprot;acc:q9una1]	Divided	238.704	255.68	1.07112	
502	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [source:swissprot;acc:p31314]	Subtracted	237.28	252.492	15.212	
503	hect domain containing protein 1 (fragment). [source:swissprot;acc:q9ult8]	Subtracted	237.28	252.492	15.212	
503	senescence marker protein-30 (smp-30) (regucalcin) (rc). [source:swissprot;acc:q15493]	Divided	238.704	255.68	1.07112	
504	homeobox protein barh-like 2. [source:swissprot;acc:q9umq3]	Subtracted	237.28	252.492	15.212	
504	oligophrenin 1. [source:swissprot;acc:o60890]	Divided	238.704	255.68	1.07112	
505	ad24 protein. [source:refseq;acc:nm_022451]	Divided	251.334	234.672	1.071	
505	zinc finger protein t86. [source:swissprot;acc:o00488]	Subtracted	246.805	231.796	15.009	
506	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [source:swissprot;acc:q9npd3]	Subtracted	215.237	230.07	14.833	
506	inhibitor of growth family, member 1; inhibitor of growth 1. [source:refseq;acc:nm_005537]	Divided	224.535	240.476	1.071	
507	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [source:swissprot;acc:q13868]	Subtracted	215.237	230.07	14.833	
507	wd-repeat protein 12 (ytm1 homolog). [source:swissprot;acc:q9gzl7]	Divided	251.299	234.729	1.07059	
508	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [source:swissprot;acc:p15088]	Divided	177.698	190.24	1.07058	
508	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	Subtracted	228.255	213.422	14.833	
509	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	Divided	177.698	190.239	1.07057	
509	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [source:swissprot;acc:q9nqt5]	Subtracted	215.237	230.07	14.833	
510	exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [source:swissprot;acc:q9nqt4]	Subtracted	215.237	230.07	14.833	
510	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [source:refseq;acc:nm_001872]	Divided	177.699	190.24	1.07057	
511	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [source:swissprot;acc:p46087]	Divided	250.053	233.725	1.06986	
511	sqv-7-like protein (fragment). [source:sptrembl;acc:o95454]	Subtracted	214.754	229.565	14.811	
512	block of proliferation 1. [source:swissprot;acc:q14137]	Divided	250.794	234.433	1.06979	
512	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [source:swissprot;acc:o43143]	Subtracted	229.803	215.301	14.502	

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/