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	Network Comparison Type	Value Type	Interaction Map	Filtered	green	red	network_comparison

Results: HTML CSV LaTeX

Showing element 151 to 200 of 6456 in total

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

Rank	description	Network Comparison Type	green	red	network_comparison
76	db83 protein. [swissprot;acc:p57088]	Divided	362	288	1.25694
	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	Subtracted	202.668	254.693	52.025
77	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	Divided		254.692	1.2567
		Subtracted			52.024
78	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]			254.691	52.023
	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	Divided		254.693	1.2567
79	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Subtracted	202.646	254.614	51.968
80	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]		242.562	294.053	51.491
	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	Divided	202.668	254.691	1.25669
81	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	Subtracted	202.016	252.371	50.355
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Divided	202.646	254.614	1.25645
82	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]		335.359	267.636	1.25304
	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807]	Subtracted	202.004	252.329	50.325
83	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]		201.998	252.309	50.311
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Divided	110.265	88.2482	1.24949
84	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]
	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	Subtracted	201.995	252.296	50.301
85	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Divided	110.265	88.2482	1.24949
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Subtracted	247.559	296.677	49.118
86	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]		286	335	49
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Divided	110.265	88.2482	1.24949
87	chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]	Subtracted	298.263	249.663	48.6
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Divided	110.265	88.2482	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	298.263	249.663	48.6
89	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Divided	110.265	88.2482	1.24949
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Subtracted	298.263	249.663	48.6
90	necdin. [swissprot;acc:q99608]	Divided	110.265	88.2482	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	298.263	249.663	48.6
91	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Divided	110.265	88.2482	1.24949
	transcription factor lbx1. [swissprot;acc:p52954]	Subtracted	298.263	249.663	48.6
92	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Divided	110.265	88.2482	1.24949
	mosaic protein lgn. [swissprot;acc:p81274]	Subtracted	298.263	249.663	48.6
93	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Divided	110.265	88.2482	1.24949
	regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6]	Subtracted	298.263	249.663	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	110.265	88.2482	1.24949
95	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
	rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736]	Subtracted	298.263	249.663	48.6
96	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]		153.671	201.949	48.278
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Divided	110.265	88.2482	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	225.68	271.752	46.072
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Divided	110.265	88.2482	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	160.957	204.641	43.684
99	jun dimerization protein. [refseq;acc:nm_130469]
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Divided	110.265	88.2482	1.24949
100	fos-related antigen 2. [swissprot;acc:p15408]	Subtracted	161.046	204.641	43.595
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Divided	110.265	88.2482	1.24949

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.