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 462 to 511 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
462	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [source:refseq;acc:nm_032390]	254.434	236.224	1.07709	
463	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [source:swissprot;acc:q9h1d9]	238.921	257.327	1.07704	
464	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [source:sptrembl;acc:q96lh6]	210.578	226.764	1.07686	
465	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	248.152	267.226	1.07686	
466	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306]	248.152	267.226	1.07686	
467	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [source:swissprot;acc:o95622]	248.152	267.226	1.07686	
468	leucine-rich repeat-containing protein 15 precursor (hlib). [source:swissprot;acc:q8tf66]	248.152	267.226	1.07686	
469	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [source:refseq;acc:nm_015322]	248.152	267.226	1.07686	
470	leucine-rich repeat protein lrrc3 precursor. [source:swissprot;acc:q9by71]	248.152	267.226	1.07686	
471	laminin gamma-1 chain precursor (laminin b2 chain). [source:swissprot;acc:p11047]	248.152	267.226	1.07686	
472	thymic stromal co-transporter. [source:refseq;acc:nm_033051]	248.152	267.226	1.07686	
473	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [source:refseq;acc:nm_015629]	225.661	209.651	1.07637	
474	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [source:swissprot;acc:p16389]	226.789	210.818	1.07576	
475	potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [source:swissprot;acc:q09470]	226.727	210.816	1.07547	
476	potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [source:swissprot;acc:p22459]	226.681	210.814	1.07527	
477	saccharomyces cerevisiae nip7p homolog. [source:refseq;acc:nm_016101]	251.926	234.547	1.0741	
478	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]	228.051	212.321	1.07409	
479	nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	228.051	212.321	1.07409	
480	neuropilin- and tolloid-like protein 2 precursor. [source:refseq;acc:nm_018092]	237.109	254.667	1.07405	
481	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [source:refseq;acc:nm_138966]	237.109	254.667	1.07405	
482	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [source:swissprot;acc:q00839]	237.109	254.667	1.07405	
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]	237.109	254.667	1.07405	
484	e1b-55kda-associated protein 5 isoform a. [source:refseq;acc:nm_007040]	237.109	254.667	1.07405	
485	60s ribosomal protein l18. [source:swissprot;acc:q07020]	237.109	254.667	1.07405	
486	mct-1 protein. [source:refseq;acc:nm_014060]	226.313	243.03	1.07387	
487	mitochondrial ribosomal protein l22. [source:refseq;acc:nm_014180]	226.313	243.03	1.07387	
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]	225.026	209.798	1.07258	
489	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [source:swissprot;acc:o75688]	231.276	215.627	1.07257	
490	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [source:swissprot;acc:q14155]	220.183	236.015	1.0719	
491	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [source:swissprot;acc:q9bze4]	251.83	234.951	1.07184	
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]	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]	220.172	235.98	1.0718	
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]	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]	220.171	235.979	1.0718	
496	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [source:swissprot;acc:q9nq55]	250.938	234.134	1.07177	
497	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [source:swissprot;acc:q99848]	251.344	234.514	1.07177	
498	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [source:swissprot;acc:q15052]	220.161	235.95	1.07172	
499	triosephosphate isomerase (ec 5.3.1.1) (tim). [source:swissprot;acc:p00938]	231.496	248.048	1.0715	
500	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [source:refseq;acc:nm_001564]	224.662	240.673	1.07127	
501	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [source:swissprot;acc:p08574]	238.704	255.68	1.07112	
502	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [source:swissprot;acc:q9una1]	238.704	255.68	1.07112	
503	senescence marker protein-30 (smp-30) (regucalcin) (rc). [source:swissprot;acc:q15493]	238.704	255.68	1.07112	
504	oligophrenin 1. [source:swissprot;acc:o60890]	238.704	255.68	1.07112	
505	ad24 protein. [source:refseq;acc:nm_022451]	251.334	234.672	1.071	
506	inhibitor of growth family, member 1; inhibitor of growth 1. [source:refseq;acc:nm_005537]	224.535	240.476	1.071	
507	wd-repeat protein 12 (ytm1 homolog). [source:swissprot;acc:q9gzl7]	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]	177.698	190.24	1.07058	
509	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	177.698	190.239	1.07057	
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]	177.699	190.24	1.07057	
511	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [source:swissprot;acc:p46087]	250.053	233.725	1.06986	

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/