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

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Showing element 825 to 874 of 3228 in total

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

green	Rank	description	network_comparison	red
194.346	548	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]	1.06645	207.26
	549	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]
	550	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631]
	552	crk-like protein. [swissprot;acc:p46109]
	553	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519]
	554	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]
	555	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]
194.347	551	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]		207.261
194.368	556	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	1.06638	207.27
194.371	557	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	1.06637	207.272
194.392	2688	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]	1.00085	194.557
194.452	559	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	1.06612	207.309
194.7	2202	tumor susceptibility gene 101 protein. [swissprot;acc:q99816]	1.00652	195.97
194.72	178	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	1.1652	226.887
194.79	179	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	1.16476	226.884
194.902	2541	aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868]	1.00204	194.505
195.064	2197	ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9]	1.00659	193.787
	2198	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [refseq;acc:nm_003679]
	2199	squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534]
195.08	2488	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	1.00284	194.527
	2489	dc11 protein. [refseq;acc:nm_020186]
	2490	amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905]
	2491	5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557]
	2492	ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968]
	2493	ubiquitin-activating enzyme e1 (a1s9 protein). [swissprot;acc:p22314]
	2494	calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746]
	2495	melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194]
	2496	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]
	2497	calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0]
	2498	acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561]
195.141	2041	ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131]	1.00854	196.808
195.173	2043	ubiquilin 1 isoform 1. [refseq;acc:nm_013438]	1.00853	196.837
195.384	2636	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	1.00128	195.635
195.385	1709	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014]	1.01346	198.014
195.386	979	gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537]	1.03399	202.027
195.466	2200	insulin gene enhancer protein isl-2 (islet-2). [swissprot;acc:q96a47]	1.00656	196.748
195.708	2314	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]	1.00496	194.743
195.787	2315	acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763]	1.00494	194.825
195.794	2317	serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743]	1.00493	194.834
	2318	sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312]
195.8	2319	acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085]	1.00492	194.842
196.061	2106	insulin gene enhancer protein isl-1 (islet-1). [swissprot;acc:p20663]	1.00728	197.489
196.252	1940	creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277]	1.00988	198.19
196.319	1939	peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347]		198.258
	1941	prp18 pre-mrna processing factor 18 homolog. [refseq;acc:nm_003675]
	1942	j domain protein c21orf55. [swissprot;acc:q9nx36]	1.00987	198.257
196.341	1938	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	1.00994	198.293
196.346	1971	creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732]	1.00974	198.258
196.347	1936	creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540]	1.00995	198.3
196.695	177	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	1.1663	229.406

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.