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

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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Network Comparison Type	Value Type	Gene	green	description	Rank	network_comparison	red	Filtered	Interaction Map

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Showing element 818 to 867 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence

green	description	Rank	network_comparison	red
194.22	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986]	2254	1.00598	193.065
194.262	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]	546	1.06671	207.222
194.328	acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067]	2643	1.00119	194.097
	atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134]	2644
	probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1]	2645
	topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027]	2642
194.346	crk-like protein. [swissprot;acc:p46109]	552	1.06645	207.26
	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]	547
	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519]	553
	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]	555
	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]	554
	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	549
	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]	548
	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631]	550
194.347	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791]	551		207.261
194.368	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	556	1.06638	207.27
194.371	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	557	1.06637	207.272
194.392	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521]	2688	1.00085	194.557
194.452	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	559	1.06612	207.309
194.7	tumor susceptibility gene 101 protein. [swissprot;acc:q99816]	2202	1.00652	195.97
194.72	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	178	1.1652	226.887
194.79	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	179	1.16476	226.884
194.902	aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868]	2541	1.00204	194.505
195.064	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [refseq;acc:nm_003679]	2198	1.00659	193.787
	squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534]	2199
	ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9]	2197
195.08	5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557]	2491	1.00284	194.527
	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]	2496
	acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561]	2498
	amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905]	2490
	calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746]	2494
	calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0]	2497
	dc11 protein. [refseq;acc:nm_020186]	2489
	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	2488
	melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194]	2495
	ubiquitin-activating enzyme e1 (a1s9 protein). [swissprot;acc:p22314]	2493
	ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968]	2492
195.141	ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131]	2041	1.00854	196.808
195.173	ubiquilin 1 isoform 1. [refseq;acc:nm_013438]	2043	1.00853	196.837
195.384	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	2636	1.00128	195.635
195.385	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014]	1709	1.01346	198.014
195.386	gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537]	979	1.03399	202.027
195.466	insulin gene enhancer protein isl-2 (islet-2). [swissprot;acc:q96a47]	2200	1.00656	196.748
195.708	ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [swissprot;acc:p51669]	2314	1.00496	194.743
195.787	acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763]	2315	1.00494	194.825
195.794	serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743]	2317	1.00493	194.834
	sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312]	2318
195.8	acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085]	2319	1.00492	194.842
196.061	insulin gene enhancer protein isl-1 (islet-1). [swissprot;acc:p20663]	2106	1.00728	197.489
196.252	creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277]	1940	1.00988	198.19

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.