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

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Showing element 1051 to 1100 of 3730 in total

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

description	Rank	Filtered	red	green	network_comparison
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	1984	1	219.26	217.193	1.00952
e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]	484		237.109	254.667	1.07405
e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	442		223.802	207.55	1.0783
eap30 subunit of ell complex. [refseq;acc:nm_007241]	163		209.299	249.187	1.19058
early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566]	1660		228.654	231.933	1.01434
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	203		201.515	228.752	1.13516
ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665]	1437		218.829	214.493	1.02022
ecotropic virus integration 1 site protein. [swissprot;acc:q03112]	3170		0.00001	0.00001	1
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	200		242.718	276.018	1.1372
eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9]	1455		207.024	211.085	1.01962
eh-domain containing protein 2. [swissprot;acc:q9nzn4]	1457			211.086
eh-domain containing protein 3. [swissprot;acc:q9nzn3]	1458
eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223]	1456
eif-5a2 protein. [refseq;acc:nm_020390]	2105		208.591	210.111	1.00729
elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127]	1538		228.419	232.376	1.01732
elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717]	1798		217.807	215.242	1.01192
elav-like protein 2 (hu-antigen b) (hub) (elav-like neuronal protein 1) (nervous system-specific rna binding protein hel-n1). [swissprot;acc:q12926]	1795		217.724	215.158	1.01193
elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	434	0	10028.5	10261.5	1.02323
	1791	1	217.866	215.295	1.01194
elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378]	1792		217.766	215.199	1.01193
electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804]	2441		180.137	180.732	1.0033
electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117]	2353		182.232	183.027	1.00436
electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134]	2016		199.092	197.301	1.00908
elks protein. [refseq;acc:nm_015064]	1061		218.162	211.648	1.03078
ell-associated factor 2; uncharacterized bone marrow protein bm040; testosterone regulated apoptosis inducer and tumor suppressor. [refseq;acc:nm_018456]	2921		0.00001	0.00001	1
elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	235	0	14554.5	16027.9	1.10123
	2433	1	217.366	218.117	1.00346
elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639]	2436
elongation factor 2 (ef-2). [swissprot;acc:p13639]	2557		222.658	223.047	1.00175
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897]	106	0	16290.7	13464.8	1.20987
	3027	1	0.00001	0.00001	1
elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60]	886		227.596	219.018	1.03917
elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040]	1802		217.011	214.481	1.0118
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759]	1322		159.86	156.275	1.02294
endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]	432		212.547	229.411	1.07934
endosome-associated fyve-domain protein. [refseq;acc:nm_014733]	3200		0.00001	0.00001	1
endothelial-derived gene 1. [refseq;acc:nm_025205]	1918		202.211	200.18	1.01015
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511]	286		224.633	203.251	1.1052
enhancer of rudimentary homolog. [swissprot;acc:q14259]	2676		214.893	215.108	1.001
enhancer of zeste homolog 1 (enx-2). [swissprot;acc:q92800]	3090		0.00001	0.00001	1
enhancer of zeste homolog 2 (enx-1). [swissprot;acc:q15910]	3098
enigma protein; lim domain protein. [refseq;acc:nm_005451]	130	0	14476.2	17069.5	1.17914
	1929	1	219.753	217.574	1.01001
enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084]	1403		184.656	180.823	1.0212
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073]	577		224.606	210.944	1.06477
enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666]	1612		221.426	224.902	1.0157
epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929]	1153		221.93	216.146	1.02676
epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204]	1152		221.939	216.143	1.02682
epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772]	1158		221.877	216.167	1.02641
epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533]	2005		225.019	222.971	1.00919

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.