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

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Showing element 2200 to 2249 of 3228 in total

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

red	green	Rank	description	network_comparison
6035.6	6464.5	1618	proteasome subunit beta type 2 (ec 3.4.25.1) (proteasome component c7-i) (macropain subunit c7-i) (multicatalytic endopeptidase complex subunit c7-i). [swissprot;acc:p49721]	1.07106
		1619	adp-ribosylation factor-like protein 1. [swissprot;acc:p40616]
6036.22	6512.64	1354	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	1.07893
6036.62	6379.38	2042	kinesin light chain 2 (klc 2). [swissprot;acc:q9h0b6]	1.05678
6036.68	6379.44	2040	rho-gtpase-activating protein 8. [swissprot;acc:q9nsg0]
		2041	rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [swissprot;acc:q07960]
		2043	kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [swissprot;acc:p33176]
		2044	kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [swissprot;acc:o60282]
		2045	neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840]
		2047	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]
		2048	exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70]
6036.73	6379.48	2046	kinesin light chain 1 (klc 1). [swissprot;acc:q07866]
6038.46	6463.9	1627	6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336]	1.07046
6042.31	6565.03	1201	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]	1.08651
6042.36	6237.19	2452	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	1.03224
6048.57	6487.65	1558	vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267]	1.07259
		1559	vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270]
		1560	vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1]
6051.06	6463.65	1725	glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744]	1.06818
6051.23	6544.17	1310	mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750]	1.08146
6057.46	6510.9	1491	fidgetin-like 1. [refseq;acc:nm_022116]	1.07486
6064.92	6421.65	2005	atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396]	1.05882
6066.61	6344.65	2295	glutathione s-transferase p (ec 2.5.1.18) (gst class-pi) (gstp1-1). [swissprot;acc:p09211]	1.04583
6068.03	6504.59	1572	proteasome subunit alpha type 1 (ec 3.4.25.1) (proteasome component c2) (macropain subunit c2) (multicatalytic endopeptidase complex subunit c2) (proteasome nu chain) (30 kda prosomal protein) (pros-30). [swissprot;acc:p25786]	1.07194
6069.65	6484.94	1717	inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218]	1.06842
6070.41	6485.85	1716	inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732]	1.06844
6072.17	6155.08	2632	histone h4. [swissprot;acc:p02304]	1.01365
6075.19	6496.61	1677	ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792]	1.06937
6075.55	6746.92	800	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406]	1.1105
6076.65	6463.64	1853	keratin associated protein 9.2. [refseq;acc:nm_031961]	1.06368
6076.66	6463.12	1865	star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2]	1.0636
		1867	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]
		1868	pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059]
		1869	integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418]
		1871	ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404]
		1872	ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283]
		1874	ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86]
		1876	espin. [refseq;acc:nm_031475]
		1877	cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635]
		1878	pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832]
		1879	lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980]
		1880	d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917]
	6463.13	1858	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]
		1859	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]
		1860	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]
		1862	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]
		1870	star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4]
	6463.14	1854	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]
		1855	keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062]
		1856	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]

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.