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

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Showing element 1001 to 1050 of 7460 in total

Value Type  : Ranked
Interaction Map  : High confidence

description	Rank	Network Comparison Type	Filtered	red	green	network_comparison
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]	364	Subtracted	0	16684	17183	499
	419	Divided				1.02991
	1928		1	196.964	198.935	1.01001
	1986	Subtracted				1.971
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]	114	Divided	0	8871.11	10603.2	1.19525
	135	Subtracted				1732.09
	1748	Divided	1	215.673	212.971	1.01269
	1756	Subtracted				2.702
bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595]	759			224.244	234.511	10.267
	793	Divided				1.04578
bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003]	3069			0.00001	0.00001	1
		Subtracted		0	0	0
bone morphogenetic protein 6 precursor (bmp-6). [swissprot;acc:p22004]	2896	Divided		0.00001	0.00001	1
		Subtracted		0	0	0
bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075]	3128	Divided		0.00001	0.00001	1
		Subtracted		0	0	0
bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]	71		0	13841.2	11127.5	2713.7
	91	Divided				1.24387
	2773		1	0.00001	0.00001	1
		Subtracted		0	0	0
brachyury protein (t protein). [swissprot;acc:o15178]	2040	Divided		210.586	208.803	1.00854
	2043	Subtracted				1.783
brain protein 16. [refseq;acc:nm_016458]	49	Divided	0	6890.54	4854.99	1.41927
	106	Subtracted				2035.55
	1835		1	216.811	219.195	2.384
	1847	Divided				1.011
brain protein 44. [swissprot;acc:o95563]	742			126.215	120.078	1.05111
	1062	Subtracted				6.137
branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687]	2672	Divided		210.957	210.741	1.00102
		Subtracted				0.216
branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382]	2681			210.939	210.755	0.184
	2687	Divided				1.00087
brca1 associated protein. [refseq;acc:nm_006768]	502		0	0.00001	0.00001	1
		Subtracted		0	0	0
	3161	Divided	1	0.00001	0.00001	1
		Subtracted		0	0	0
brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728]	1745			216.271	218.991	2.72
	1752	Divided				1.01258
brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567]	209	Subtracted		240.782	265.717	24.935
	294	Divided				1.10356
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	229			226.401	202.094	1.12028
	232	Subtracted				24.307
breast cancer type 1 susceptibility protein. [swissprot;acc:p38398]	920			216.501	224.27	7.769
	939	Divided				1.03588
breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]	691			217.602	206.195	1.05532
	693	Subtracted				11.407
brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6]	2705			220.521	220.395	0.126
	2713	Divided				1.00057
brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5]	2703	Subtracted				0.126
	2711	Divided				1.00057

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.