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

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Showing element 601 to 650 of 77072 in total

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red	green	description	Rank	Interaction Map	Value Type	network_comparison	Network Comparison Type
7.79521	7.32908	glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409]	317	High confidence	Rooted	1.0636	Divided
			438			0.46613	Subtracted
7.80086	7.3344	glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189]	318			1.0636	Divided
			437			0.46646	Subtracted
7.8774	1.68817	tubulointerstitial nephritis antigen. [refseq;acc:nm_014464]	53	Low confidence	Squared	4.66624	Divided
			765			6.18923	Subtracted
7.90063	14.4058	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	25		Rooted	1.82337	Divided
			34			6.50517	Subtracted
			39	High confidence		1.82337	Divided
			67			6.50517	Subtracted
7.9671	10.6057	nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505]	90	Low confidence		1.33119	Divided
			309			2.6386	Subtracted
7.96876	10.6064	nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8]	91			1.331	Divided
			310			2.63764	Subtracted
8.0312	7.85784	tubulointerstitial nephritis antigen. [refseq;acc:nm_014464]	689			1.02206	Divided
			787			0.17336	Subtracted
8.05424	8.90701	ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]	253	High confidence		1.10588	Divided
			392			0.85277	Subtracted
		ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]	254			1.10588	Divided
			393			0.85277	Subtracted
8.10857	43.7473	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]	49		Squared	5.39519	Divided
			351			35.6387	Subtracted
8.11997	115.385	fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344]	13	Low confidence	Measured	14.21	Divided
			423			107.265	Subtracted
8.12404	6.08276	arf gtpase-activating protein. [refseq;acc:nm_133446]	87		Rooted	1.33558	Divided
			365			2.04128	Subtracted
		up-regulated in liver cancer 1; similar to development- and differentiation-enhancing factor 2. [refseq;acc:nm_017707]	88			1.33558	Divided
			366			2.04128	Subtracted
8.14325	6.488	sarcoplasmic/endoplasmic reticulum calcium atpase 1 (ec 3.6.3.8) (calcium pump 1) (serca1) (sr ca(2+)-atpase 1) (calcium-transporting atpase sarcoplasmic reticulum type, fast twitch skeletal muscle isoform) (endoplasmic reticulum class 1/2 ca(2+) atpase). [swissprot;acc:o14983]	112			1.25512	Divided
			436			1.65525	Subtracted
8.15919	4.74982	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	146	High confidence	Squared	1.71779	Divided
			424			3.40937	Subtracted
8.27667	5.86733	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	206			1.41064	Divided
			434			2.40934	Subtracted
8.27669	4.90793	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	149			1.68639	Divided
			425			3.36876	Subtracted
8.45575	8.33665	pou domain, class 3, transcription factor 3 (brain-specific homeobox/pou domain protein 1) (brain-1) (brn-1 protein). [swissprot;acc:p20264]	736	Low confidence	Rooted	1.01429	Divided
			802			0.1191	Subtracted
8.48528	12.2882	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	60	High confidence		1.44818	Divided
			63	Low confidence
			144	High confidence		3.80292	Subtracted
			225	Low confidence
8.52047	10.0173	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]	148	High confidence		1.17567	Divided
			318			1.49683	Subtracted
		interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	146	Low confidence		1.17567	Divided
			149	High confidence
			319			1.49683	Subtracted
			469	Low confidence
8.7178	9.74679	protein c20orf142 precursor. [swissprot;acc:q8n6m3]	226			1.11803	Divided
			573			1.02899	Subtracted

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.