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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 958 to 1007 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
479	nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	Divided	228.051	212.321	1.07409	
480	neuropilin- and tolloid-like protein 2 precursor. [source:refseq;acc:nm_018092]	Divided	237.109	254.667	1.07405	
480	serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [source:swissprot;acc:q13153]	Subtracted	220.172	235.98	15.808	
481	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [source:refseq;acc:nm_138966]	Divided	237.109	254.667	1.07405	
481	serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [source:swissprot;acc:o75914]	Subtracted	220.171	235.979	15.808	
482	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [source:swissprot;acc:q00839]	Divided	237.109	254.667	1.07405	
482	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [source:swissprot;acc:q15052]	Subtracted	220.161	235.95	15.789	
483	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [source:swissprot;acc:q13950]	Divided	237.109	254.667	1.07405	
483	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [source:swissprot;acc:q92994]	Subtracted	228.051	212.321	15.73	
484	e1b-55kda-associated protein 5 isoform a. [source:refseq;acc:nm_007040]	Divided	237.109	254.667	1.07405	
484	nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	Subtracted	228.051	212.321	15.73	
485	60s ribosomal protein l18. [source:swissprot;acc:q07020]	Divided	237.109	254.667	1.07405	
485	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [source:swissprot;acc:o75688]	Subtracted	231.276	215.627	15.649	
486	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [source:swissprot;acc:p56537]	Subtracted	248.866	233.287	15.579	
486	mct-1 protein. [source:refseq;acc:nm_014060]	Divided	226.313	243.03	1.07387	
487	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [source:swissprot;acc:p40926]	Subtracted	238.529	254.099	15.57	
487	mitochondrial ribosomal protein l22. [source:refseq;acc:nm_014180]	Divided	226.313	243.03	1.07387	
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	

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/