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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 982 to 1031 of 3730 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	red	green	network_comparison	
491	rwd domain containing 1; ptd013 protein; cgi-24 protein. [source:refseq;acc:nm_015952]	0	21970	21880	1.00411	
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]	1	220.171	235.979	1.0718	
492	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [source:swissprot;acc:q96gm5]	0	6802.96	6829.74	1.00394	
493	conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [source:swissprot;acc:q9up83]	1	220.172	235.98	1.0718	
493	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [source:sptrembl;acc:q9h5b6]	0	11999.1	12041.7	1.00355	
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]	1	220.172	235.98	1.0718	
494	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [source:swissprot;acc:p08240]	0	11985.5	11959.4	1.00218	
495	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	0	11725.2	11748.1	1.00195	
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]	1	220.171	235.979	1.0718	
496	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [source:swissprot;acc:q9nq55]	1	250.938	234.134	1.07177	
496	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [source:swissprot;acc:o95670]	0	9394	9411.49	1.00186	
497	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [source:swissprot;acc:q99848]	1	251.344	234.514	1.07177	
497	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [source:refseq;acc:nm_014633]	0	13692.7	13718.2	1.00186	
498	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p27144]	0	10231.8	10248.3	1.00161	
498	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [source:swissprot;acc:q15052]	1	220.161	235.95	1.07172	
499	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [source:swissprot;acc:p12268]	0	9080.73	9069.58	1.00123	
499	triosephosphate isomerase (ec 5.3.1.1) (tim). [source:swissprot;acc:p00938]	1	231.496	248.048	1.0715	
500	huntingtin interacting protein e; huntingtin interactor protein e. [source:refseq;acc:nm_007076]	0	394	394	1	
500	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [source:refseq;acc:nm_001564]	1	224.662	240.673	1.07127	
501	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [source:swissprot;acc:p08574]	1	238.704	255.68	1.07112	
501	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	0	0.00001	0.00001	1	
502	brca1 associated protein. [source:refseq;acc:nm_006768]	0	0.00001	0.00001	1	
502	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [source:swissprot;acc:q9una1]	1	238.704	255.68	1.07112	
503	senescence marker protein-30 (smp-30) (regucalcin) (rc). [source:swissprot;acc:q15493]	1	238.704	255.68	1.07112	
504	oligophrenin 1. [source:swissprot;acc:o60890]	1	238.704	255.68	1.07112	
505	ad24 protein. [source:refseq;acc:nm_022451]	1	251.334	234.672	1.071	
506	inhibitor of growth family, member 1; inhibitor of growth 1. [source:refseq;acc:nm_005537]	1	224.535	240.476	1.071	
507	wd-repeat protein 12 (ytm1 homolog). [source:swissprot;acc:q9gzl7]	1	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]	1	177.698	190.24	1.07058	
509	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	1	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]	1	177.699	190.24	1.07057	
511	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [source:swissprot;acc:p46087]	1	250.053	233.725	1.06986	
512	block of proliferation 1. [source:swissprot;acc:q14137]	1	250.794	234.433	1.06979	
513	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	1	218.596	204.344	1.06975	
514	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	1	218.613	204.382	1.06963	
515	pescadillo homolog 1. [source:swissprot;acc:o00541]	1	251.297	234.941	1.06962	
516	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	1	228.255	213.422	1.0695	
517	metaxin 2. [source:swissprot;acc:o75431]	1	219.537	234.793	1.06949	
518	nucleostemin; putative nucleotide binding protein, estradiol-induced. [source:refseq;acc:nm_014366]	1	250.858	234.563	1.06947	
519	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	1	218.702	204.582	1.06902	
520	sqv-7-like protein (fragment). [source:sptrembl;acc:o95454]	1	214.754	229.565	1.06897	
521	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [source:swissprot;acc:q9npd3]	1	215.237	230.07	1.06891	
522	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	1	222.893	208.523	1.06891	
523	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [source:swissprot;acc:q13868]	1	215.237	230.07	1.06891	
524	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [source:swissprot;acc:q9nqt5]	1	215.237	230.07	1.06891	
525	exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [source:swissprot;acc:q9nqt4]	1	215.237	230.07	1.06891	
526	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [source:swissprot;acc:p56182]	1	250.538	234.401	1.06884	
527	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [source:refseq;acc:nm_022779]	1	248.56	232.579	1.06871	
528	yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [source:refseq;acc:nm_014263]	1	222.146	237.393	1.06864	
529	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [source:swissprot;acc:q9nvp1]	1	251.653	235.506	1.06856	

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/