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	Gene	red	green	Value Type	Rank	Interaction Map	description	Filtered	network_comparison

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Showing element 2458 to 2507 of 3228 in total

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

red	green	Rank	description	network_comparison
6297.05	6721.08	1741	serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075]	1.06734
6298.76	6722.61	1742	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	1.06729
6298.77	6722.62	1745	microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8]
6298.81	6722.65	1743	histidine-rich membrane protein ke4. [swissprot;acc:q92504]
		1744	microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691]
6301.03	6724.63	1748	doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602]	1.06723
6304.21	6738.77	1697	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	1.06893
		1699	rest corepressor. [refseq;acc:nm_015156]
6304.22		1696	wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5]
		1698	wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558]
6304.74	6740.66	1681	f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2]	1.06914
		1682	f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756]
6311.6	6989.33	822	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	1.10738
6311.83	6989.6	823	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]
6318.3	6670.1	2081	paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367]	1.05568
6322.75	6820.5	1362	sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900]	1.07872
		1363	nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307]
6324.31	6948.5	921	translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199]	1.0987
6326.24	6762.27	1700	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747]	1.06892
		1701	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]
		1702	dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690]
		1703	phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645]
6327.14	6579.38	2389	lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234]	1.03987
		2390	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]
		2391	defender against cell death 1 (dad-1). [swissprot;acc:p46966]
		2392	t-complex 11. [refseq;acc:nm_018679]
		2393	tubulin gamma-2 chain (gamma-2 tubulin). [swissprot;acc:q9nrh3]
6327.86	7064.13	726	dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1]	1.11635
6334.15	6852.61	1303	cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441]	1.08185
6336.22	6788.96	1600	14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758]	1.07145
6339.08	6812.45	1497	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]	1.07467
6340.5	6815.41	1490	f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907]	1.0749
6343.26	6862.94	1302	peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162]	1.08193
6343.76	6803.44	1565	proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787]	1.07246
6344.31	6657.98	2198	complement component 1, q subcomponent binding protein, mitochondrial precursor (glycoprotein gc1qbp) (gc1q-r protein) (hyaluronan-binding protein 1) (p32) (p33). [swissprot;acc:q07021]	1.04944
		2199	sirtuin 1; sir2-like 1; sirtuin type 1; sir2alpha; sirtuin silent mating type information regulation 2 homolog 1 (s. cerevisiae). [refseq;acc:nm_012238]
6344.41	6933.36	1043	15 kda selenoprotein precursor. [swissprot;acc:o60613]	1.09283
6349.23	6406.72	2653	tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890]	1.00905
6349.55	6407.25	2652	tumor protein d52 (n8 protein). [swissprot;acc:p55327]	1.00909
6350.81	6874.88	1280	dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887]	1.08252
6351.32	6805.39	1595	proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062]	1.07149
6360.13	6825.36	1540	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	1.07315
6362.48	6647.42	2319	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231]	1.04478
		2320	t54 protein. [swissprot;acc:q92917]
6362.64	6976.1	984	integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287]	1.09642
		985	integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7]
		986	integral membrane protein 2a (e25 protein). [swissprot;acc:o43736]
6362.92	6838.6	1495	nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [swissprot;acc:o96000]	1.07476
6364.01	6819.38	1590	fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281]	1.07155
		1591	multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155]

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.