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

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Showing element 3132 to 3181 of 3228 in total

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

description	Rank	red	green	network_comparison
vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065]	2152	200.063	198.71	1.00681
vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836]	2157
vesicle-associated membrane protein-associated protein a (vamp- associated protein a) (vamp-a) (vap-a) (33 kda vamp-associated protein) (vap-33). [swissprot;acc:q9p0l0]	3123	0.00001	0.00001	1
vesicle-associated membrane protein-associated protein b/c (vamp- associated protein b/c) (vamp-b/vamp-c) (vap-b/vap-c). [swissprot;acc:o95292]	3023
vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459]	2457	213.588	212.92	1.00314
vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379]	2154	200.063	198.71	1.00681
vinculin (metavinculin). [swissprot;acc:p18206]	999	215.92	208.95	1.03336
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	956	211.812	204.732	1.03458
visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235]	1185	225.094	230.913	1.02585
voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	77	254.692	202.668	1.2567
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	79	254.693
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	80	254.691		1.25669
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	81	254.614	202.646	1.25645
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	78	254.693	202.668	1.2567
voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722]	1956	211.633	213.703	1.00978
voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303]	1968
voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448]	1954	211.632		1.00979
vps28 protein homolog. [swissprot;acc:q9uk41]	2871	0.00001	0.00001	1
wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830]	1407	206.104	210.424	1.02096
wd repeat domain 26. [refseq;acc:nm_025160]	1429	213.351	217.74	1.02057
wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950]	1410	206.1	210.417	1.02095
wd-repeat containing protein ciao 1. [swissprot;acc:o76071]	2927	0.00001	0.00001	1
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7]	507	251.299	234.729	1.07059
wd-repeat protein 3. [swissprot;acc:q9unx4]	912	243.896	234.96	1.03803
wd-repeat protein 4. [swissprot;acc:p57081]	2217	221.509	220.108	1.00637
wd-repeat protein bing4. [swissprot;acc:o15213]	1008	243.227	235.475	1.03292
wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	853	108.289	112.772	1.0414
werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135]	1325	217.133	212.289	1.02282
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]	1876	223.862	226.271	1.01076
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]	1875
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]	3218	0.00001	0.00001	1
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	1874	223.862	226.271	1.01076
wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007]	2625	204.304	204.028	1.00135
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]	546	207.222	194.262	1.06671
wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558]	1975	214.611	212.546	1.00972
wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5]	1973
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	1974
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516]	825	206.214	197.614	1.04352
wnt1 inducible signaling pathway protein 1 isoform 1 precursor; wnt-1 signaling pathway protein 1; wnt1 signaling pathway protein 1; wnt-1 inducible signaling pathway protein 1. [refseq;acc:nm_003882]	3109	0.00001	0.00001	1
wnt1 inducible signaling pathway protein 3 isoform 1; wnt-1 signaling pathway protein 3; wnt1 signaling pathway protein 3; wnt-1 inducible signaling pathway protein 3. [refseq;acc:nm_003880]	3065
ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312]	1537	228.419	232.376	1.01732
ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9]	1073	216.901	210.485	1.03048
xanthine dehydrogenase/oxidase [includes: xanthine dehydrogenase (ec 1.1.1.204) (xd); xanthine oxidase (ec 1.1.3.22) (xo) (xanthine oxidoreductase)]. [swissprot;acc:p47989]	2882	0.00001	0.00001	1
xap-5 protein (hxc-26 protein). [swissprot;acc:q14320]	1685	216.899	213.889	1.01407
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736]	856	215.028	206.623	1.04068
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	9	212	309	1.45755
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7]	738	222.825	211.966	1.05123
xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385]	2328	209.326	208.357	1.00465
xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108]	2476	211.205	210.577	1.00298
yeast sec31p homolog. [refseq;acc:nm_014933]	1136	218.484	212.675	1.02731

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.