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

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Showing element 182 to 231 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
91	transcription factor lbx1. [swissprot;acc:p52954]	Subtracted	249.663	298.263	48.6
92	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Divided	88.2482	110.265	1.24949
	mosaic protein lgn. [swissprot;acc:p81274]	Subtracted	249.663	298.263	48.6
93	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Divided	88.2482	110.265	1.24949
	regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6]	Subtracted	249.663	298.263	48.6
94	guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471]
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Divided	88.2482	110.265	1.24949
95	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
	rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736]	Subtracted	249.663	298.263	48.6
96	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]		201.949	153.671	48.278
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Divided	88.2482	110.265	1.24949
97	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	Subtracted	271.752	225.68	46.072
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Divided	88.2482	110.265	1.24949
98	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	Subtracted	204.641	160.957	43.684
99	jun dimerization protein. [refseq;acc:nm_130469]
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Divided	88.2482	110.265	1.24949
100	fos-related antigen 2. [swissprot;acc:p15408]	Subtracted	204.641	161.046	43.595
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Divided	88.2482	110.265	1.24949
101	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Subtracted	204.641	161.051	43.59
102	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]		204.642	161.068	43.574
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	Divided	88.2482	110.265	1.24949
103	transcription factor jun-b. [swissprot;acc:p17275]	Subtracted	201.144	158.868	42.276
	trophinin. [swissprot;acc:q12816]	Divided	88.2482	110.265	1.24949
104	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]		252.371	202.016	1.24926
	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Subtracted	256.228	298.438	42.21
105	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]	Divided	266.716	333.165	1.24914
	transcription factor jun-d. [swissprot;acc:p17535]	Subtracted	200.941	158.941	42
106	nostrin. [refseq;acc:nm_052946]		209.299	249.187	39.888
	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807]	Divided	252.329	202.004	1.24913
107	eap30 subunit of ell complex. [refseq;acc:nm_007241]	Subtracted	209.299	249.187	39.888
	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	Divided	252.309	201.998	1.24907
108	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]		252.296	201.995	1.24902
	liv-1 protein, estrogen regulated. [refseq;acc:nm_012319]	Subtracted	209.299	249.187	39.888
109	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]
	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	Divided	266.933	333.281	1.24856
110	deltex 2. [refseq;acc:nm_020892]		333.144	267.393	1.2459
	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747]	Subtracted	209.299	249.187	39.888
111	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Divided	332.925	267.274	1.24563
	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259]	Subtracted	209.299	249.187	39.888
112	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]		275.754	235.908	39.846
	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	Divided	332.874	267.246	1.24557
113	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]
	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	Subtracted	194.372	234.204	39.832
114	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]		229.818	267.265	37.447
	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	Divided	332.874	267.246	1.24557
115	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	Subtracted	277.546	240.461	37.085
	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Divided	332.874	267.246	1.24557
116	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]		268.565	334.483	1.24545

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.