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

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Showing element 882 to 931 of 3228 in total

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

description	Rank	red	green	network_comparison
dual specificity protein phosphatase 11 (ec 3.1.3.48) (rna/rnp complex-intereracting phosphatase) (phosphatase that interacts with rna/rnp complex 1). [swissprot;acc:o75319]	2926	0.00001	0.00001	1
dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [swissprot;acc:q13627]	1800	217.011	214.481	1.0118
dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463]	1803
dymeclin. [refseq;acc:nm_017653]	2055	218.79	216.981	1.00834
dynactin 4. [refseq;acc:nm_032486]	426	233.142	252.253	1.08197
dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561]	1549	225.159	221.424	1.01687
dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690]	2081	215.967	214.28	1.00787
dynein 2 light intermediate chain. [refseq;acc:nm_016008]	2962	0.00001	0.00001	1
dynein intermediate chain 1, axonemal (axonemal dynein intermediate chain 1). [swissprot;acc:q9ui46]	3029
dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	1005	225.448	218.232	1.03307
dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	998	225.557	218.271	1.03338
dynein light chain 2. [refseq;acc:nm_080677]	647	216.731	229.549	1.05914
dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	1085	231.007	237.864	1.02968
dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8]	2583	213.415	213.743	1.00154
dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941]	2581	213.428	213.756
dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	1599	217.871	214.404	1.01617
dystrophin. [swissprot;acc:p11532]	2584	213.422	213.75	1.00154
e-1 enzyme. [refseq;acc:nm_021204]	2251	208.315	207.061	1.00606
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	1984	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]	1791	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]	2433	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]	3027	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

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.