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 168 to 217 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
84	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	Subtracted	252.296	201.995	50.301
85	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Divided	88.2482	110.265	1.24949
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Subtracted	296.677	247.559	49.118
86	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]		335	286	49
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Divided	88.2482	110.265	1.24949
87	chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]	Subtracted	249.663	298.263	48.6
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Divided	88.2482	110.265	1.24949
88	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]	Subtracted	249.663	298.263	48.6
89	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Divided	88.2482	110.265	1.24949
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Subtracted	249.663	298.263	48.6
90	necdin. [swissprot;acc:q99608]	Divided	88.2482	110.265	1.24949
	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081]	Subtracted	249.663	298.263	48.6
91	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Divided	88.2482	110.265	1.24949
	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]

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.