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	Filtered	Interaction Map	network_comparison	red	green

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Showing element 580 to 629 of 3228 in total

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

description	Rank	network_comparison	red	green
chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	330	1.09859	312	284
chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824]	2553	1.0018	193.12	193.467
chromodomain y-like protein 2. [refseq;acc:nm_152342]	2556	1.00177	193.119	193.46
chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265]	1211	1.02517	214.364	219.759
chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]	153	1.19466	249.663	298.263
cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]	982	1.03383	243.312	235.351
cisplatin resistance related protein crr9p. [refseq;acc:nm_030782]	3197	1	0.00001	0.00001
clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641]	1392	1.02148	218.471	213.876
clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172]	2208	1.00645	199.129	200.413
clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	399	1.08821	207.889	226.226
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	405	1.0879	207.931	226.209
cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	850	1.04161	107.842	112.329
cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006]	1657	1.01443	219.314	216.195
cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007]	1480	1.01918	218.664	214.55
cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	871	1.03949	110.2	114.552
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	854	1.0414	108.289	112.772
cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	1006	1.03305	116.524	120.375
cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	1089	1.02945	121.428	125.004
cleavage stimulation factor, 50 kda subunit (cstf 50 kda subunit) (cf-1 50 kda subunit). [swissprot;acc:q05048]	3129	1	0.00001	0.00001
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	2140	1.00692	161.547	162.665
cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]	756	1.04968	224.434	235.583
clll6 protein. [refseq;acc:nm_020456]	3028	1	0.00001	0.00001
coactosin-like protein. [swissprot;acc:q14019]	1219	1.025	211.959	217.258
coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621]	1093	1.02939	177.432	182.647
coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618]	1036	1.03155	171.341	176.746
coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	1074	1.03045	174.387	179.697
coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444]	1077
coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579]	1174	1.02599	187.964	192.849
coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678]	1075	1.03045	174.387	179.697
coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3]	1076
coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]	1079
cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281]	2227	1.00634	217.955	219.336
cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528]	2226
collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955]	1989	1.00951	219.261	217.195
collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	1990		219.26	217.194
collectin sub-family member 12 isoform i; scavenger receptor with c-type lectin; collectin placenta 1; scavenger receptor class a, member 4. [refseq;acc:nm_130386]	2881	1	0.00001	0.00001
colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508]	1402	1.0212	209.682	205.329
complement component 1, q subcomponent binding protein, mitochondrial precursor (glycoprotein gc1qbp) (gc1q-r protein) (hyaluronan-binding protein 1) (p32) (p33). [swissprot;acc:q07021]	2730	1.0003	212.922	212.985
complement component c6 precursor. [swissprot;acc:p13671]	3199	1	0.00001	0.00001
complement component c7 precursor. [swissprot;acc:p10643]	3064
complement component c8 alpha chain precursor. [swissprot;acc:p07357]	2886
complement component c8 beta chain precursor. [swissprot;acc:p07358]	3207
complement component c9 precursor. [swissprot;acc:p02748]	3057
cone-rod homeobox protein. [swissprot;acc:o43186]	1519	1.01779	244.331	240.061
connective tissue growth factor precursor (hypertrophic chondrocyte- specific protein 24). [swissprot;acc:p29279]	3040	1	0.00001	0.00001
connective tissue growth factor-like protein precursor (ctgf-l) (wnt1 inducible signaling pathway protein 2) (wisp-2) (connective tissue growth factor-related protein 58). [swissprot;acc:o76076]	3188
conserved oligomeric golgi complex component 1. [swissprot;acc:q8wtw3]	2836
conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746]	1213	1.02517	214.364	219.759
conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2]	2627	1.00135	224.891	225.195
conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7]	2110	1.00712	211.099	209.607

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.