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

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Showing element 501 to 550 of 77072 in total

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network_comparison	green	description	Interaction Map	Value Type	Network Comparison Type	Rank	red
0.9646	24.3289	40s ribosomal protein s12. [swissprot;acc:p25398]	Low confidence	Rooted	Subtracted	593	23.3643
0.965708	1.63441	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	High confidence	Squared		447	0.668702
0.9672	17.4854	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]		Rooted		381	16.5182
0.9753	43.0082	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]				380	42.0329
		histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]				379
0.9767	16.5084	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]	Low confidence			592	15.5317
0.9771	33.4964	neprilysin (ec 3.4.24.11) (neutral endopeptidase) (nep) (enkephalinase) (common acute lymphocytic leukemia antigen) (calla) (neutral endopeptidase 24.11) (cd10). [swissprot;acc:p08473]				591	34.4735
0.9803	19.119	ba161i19.3 (similar to ribosomal protein l36). [sptrembl;acc:q8wx03]				590	18.1387
0.9827	25.6434	rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]				589	24.6607
0.9843	19.2328	kappa b-ras 1. [refseq;acc:nm_020345]				588	20.2171
0.9856	33.9829	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]				587	34.9685
0.9892	26.8952	60s ribosomal protein l9. [swissprot;acc:p32969]				586	25.906
0.98968	6.55744	methyltransferase like 2. [refseq;acc:nm_018396]	High confidence			378	5.56776
0.9907	29.8694	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]				377	30.8601
0.995	26.0677	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	Low confidence			585	27.0627
1	0.00001	brca1 associated protein. [refseq;acc:nm_006768]	High confidence	Measured	Divided	502	0.00001
				Ranked
				Squared
				Rooted
		cobw-like protein. [refseq;acc:nm_018491]	Low confidence	Measured		839
				Ranked
				Squared
				Rooted
		gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]		Measured		838
				Ranked
				Squared
				Rooted
		gamma-glutamyltransferase. [sptrembl;acc:q14390]		Measured		841
				Ranked
				Squared
				Rooted
		gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]		Measured		842
				Ranked
				Squared
				Rooted
		gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]		Measured		837
				Ranked
				Squared
				Rooted
		gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]		Measured		843
				Ranked
				Squared
				Rooted
		h2a histone family, member j isoform 1. [refseq;acc:nm_018267]	High confidence	Measured		501
				Squared
				Rooted
		histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]		Measured		495
				Squared
				Rooted
		histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]		Measured		494

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.