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

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Showing element 868 to 917 of 3228 in total

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

description	Rank	green	red	network_comparison
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	221.28	1.03205
double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959]	1046	178.889	173.475	1.03121
double-stranded rna-binding zinc finger protein jaz. [refseq;acc:nm_012279]	3054	0.00001	0.00001	1
doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602]	2725	216.569	216.496	1.00034
doublesex and mab-3 related transcription factor 3; testis-specific protein; dmrt-like family a3. [refseq;acc:nm_021240]	3187	0.00001	0.00001	1
down-regulated in metastasis. [refseq;acc:nm_014503]	787	233.508	244.447	1.04685
dpy-30-like protein. [swissprot;acc:q9c005]	1815	217.926	220.462	1.01164
dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442]	1468	207.937	212.001	1.01954
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	217.555	1.0081
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	210.595	1.00395
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	220.076	1.00468
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	210.57	1.00397
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	221.248	1.00696
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	214.481	217.011	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	216.981	218.79	1.00834
dynactin 4. [refseq;acc:nm_032486]	426	252.253	233.142	1.08197
dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561]	1549	221.424	225.159	1.01687
dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690]	2081	214.28	215.967	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	218.232	225.448	1.03307
dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	998	218.271	225.557	1.03338
dynein light chain 2. [refseq;acc:nm_080677]	647	229.549	216.731	1.05914
dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	1085	237.864	231.007	1.02968
dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8]	2583	213.743	213.415	1.00154
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	217.871	1.01617
dystrophin. [swissprot;acc:p11532]	2584	213.75	213.422	1.00154
e-1 enzyme. [refseq;acc:nm_021204]	2251	207.061	208.315	1.00606
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	1984	217.193	219.26	1.00952
e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]	484	254.667	237.109	1.07405
e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	442	207.55	223.802	1.0783
eap30 subunit of ell complex. [refseq;acc:nm_007241]	163	249.187	209.299	1.19058
early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566]	1660	231.933	228.654	1.01434
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	203	228.752	201.515	1.13516
ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665]	1437	214.493	218.829	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	276.018	242.718	1.1372
eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9]	1455	211.085	207.024	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	210.111	208.591	1.00729
elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127]	1538	232.376	228.419	1.01732
elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717]	1798	215.242	217.807	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	215.158	217.724	1.01193
elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	1791	215.295	217.866	1.01194

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.