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	Value Type	Gene	description	Rank	green	network_comparison	red	Filtered	Interaction Map

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Showing element 868 to 917 of 3228 in total

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

description	Rank	green	network_comparison	red
dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126]	1020	214.409	1.03205	221.28
double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959]	1046	178.889	1.03121	173.475
double-stranded rna-binding zinc finger protein jaz. [refseq;acc:nm_012279]	3054	0.00001	1	0.00001
doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602]	2725	216.569	1.00034	216.496
doublesex and mab-3 related transcription factor 3; testis-specific protein; dmrt-like family a3. [refseq;acc:nm_021240]	3187	0.00001	1	0.00001
down-regulated in metastasis. [refseq;acc:nm_014503]	787	233.508	1.04685	244.447
dpy-30-like protein. [swissprot;acc:q9c005]	1815	217.926	1.01164	220.462
dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442]	1468	207.937	1.01954	212.001
dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750]	2069	215.807	1.0081	217.555
dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507]	2072
dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [swissprot;acc:p46734]	2385	209.767	1.00395	210.595
dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985]	2326	219.05	1.00468	220.076
dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [swissprot;acc:p52564]	2384	209.737	1.00397	210.57
dual specificity mitogen-activated protein kinase kinase 7 (ec 2.7.1.-) (map kinase kinase 7) (mapkk 7) (mapk/erk kinase 7) (jnk activating kinase 2) (c-jun n-terminal kinase kinase 2) (jnk kinase 2) (jnkk 2). [swissprot;acc:o14733]	2139	222.788	1.00696	221.248
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	1	0.00001
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	214.481	1.0118	217.011
dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463]	1803
dymeclin. [refseq;acc:nm_017653]	2055	216.981	1.00834	218.79
dynactin 4. [refseq;acc:nm_032486]	426	252.253	1.08197	233.142
dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561]	1549	221.424	1.01687	225.159
dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690]	2081	214.28	1.00787	215.967
dynein 2 light intermediate chain. [refseq;acc:nm_016008]	2962	0.00001	1	0.00001
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	218.232	1.03307	225.448
dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	998	218.271	1.03338	225.557
dynein light chain 2. [refseq;acc:nm_080677]	647	229.549	1.05914	216.731
dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	1085	237.864	1.02968	231.007
dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8]	2583	213.743	1.00154	213.415
dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941]	2581	213.756		213.428
dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	1599	214.404	1.01617	217.871
dystrophin. [swissprot;acc:p11532]	2584	213.75	1.00154	213.422
e-1 enzyme. [refseq;acc:nm_021204]	2251	207.061	1.00606	208.315
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	1984	217.193	1.00952	219.26
e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]	484	254.667	1.07405	237.109
e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	442	207.55	1.0783	223.802
eap30 subunit of ell complex. [refseq;acc:nm_007241]	163	249.187	1.19058	209.299
early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566]	1660	231.933	1.01434	228.654
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	203	228.752	1.13516	201.515
ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665]	1437	214.493	1.02022	218.829
ecotropic virus integration 1 site protein. [swissprot;acc:q03112]	3170	0.00001	1	0.00001
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	200	276.018	1.1372	242.718
eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9]	1455	211.085	1.01962	207.024
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	210.111	1.00729	208.591
elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127]	1538	232.376	1.01732	228.419
elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717]	1798	215.242	1.01192	217.807
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	215.158	1.01193	217.724
elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	1791	215.295	1.01194	217.866

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.