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 - 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 964 to 1013 of 3730 in total

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

Rank	description	Filtered	red	green	network_comparison
482	kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]	0	6156.33	6205.67	1.00801
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). [swissprot;acc:q13950]	1	237.109	254.667	1.07405
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	0	12223.8	12127.5	1.00794
484	e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]	1	237.109	254.667	1.07405
	protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1]	0	11489.7	11414.3	1.00661
485	60s ribosomal protein l18. [swissprot;acc:q07020]	1	237.109	254.667	1.07405
	pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790]	0	12461.5	12542.3	1.00648
486	huntingtin interacting protein c. [refseq;acc:nm_012272]		13372.4	13288.3	1.00633
	mct-1 protein. [refseq;acc:nm_014060]	1	226.313	243.03	1.07387
487	mitochondrial ribosomal protein l22. [refseq;acc:nm_014180]
	survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]	0	13236.8	13159.3	1.00589
488	heat shock factor binding protein 1. [swissprot;acc:o75506]		15204.2	15127.8	1.00505
	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. [refseq;acc:nm_005146]	1	225.026	209.798	1.07258
489	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	0	8854.04	8811.09	1.00487
	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688]	1	231.276	215.627	1.07257
490	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	0	10388.7	10338.7	1.00484
	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155]	1	220.183	236.015	1.0719
491	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]		251.83	234.951	1.07184
	rwd domain containing 1; ptd013 protein; cgi-24 protein. [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). [swissprot;acc:q13177]	1	220.171	235.979	1.0718
	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [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). [swissprot;acc:q9up83]	1	220.172	235.98	1.0718
	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [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). [swissprot;acc:q13153]	1	220.172	235.98	1.0718
	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	0	11985.5	11959.4	1.00218
495	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]		11725.2	11748.1	1.00195
	serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914]	1	220.171	235.979	1.0718
496	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]		250.938	234.134	1.07177
	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). [swissprot;acc:o95670]	0	9394	9411.49	1.00186
497	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	1	251.344	234.514	1.07177
	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [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). [swissprot;acc:p27144]		10231.8	10248.3	1.00161
	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [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). [swissprot;acc:p12268]	0	9080.73	9069.58	1.00123
	triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938]	1	231.496	248.048	1.0715
500	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	0	394	394	1
	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564]	1	224.662	240.673	1.07127
501	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574]		238.704	255.68	1.07112
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0	0.00001	0.00001	1
502	brca1 associated protein. [refseq;acc:nm_006768]
	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]	1	238.704	255.68	1.07112
503	senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493]
504	oligophrenin 1. [swissprot;acc:o60890]
505	ad24 protein. [refseq;acc:nm_022451]		251.334	234.672	1.071
506	inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537]		224.535	240.476
507	wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7]		251.299	234.729	1.07059
508	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]		177.698	190.24	1.07058
509	carboxypeptidase b precursor. [refseq;acc:nm_020361]			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. [refseq;acc:nm_001872]		177.699	190.24
511	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]		250.053	233.725	1.06986

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.