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	description	green	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	description	green	Rank	Interaction Map	Value Type	network_comparison	Network Comparison Type
7.79521	glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409]	7.32908	317	High confidence	Rooted	1.0636	Divided
			438			0.46613	Subtracted
7.80086	glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189]	7.3344	318			1.0636	Divided
			437			0.46646	Subtracted
7.8774	tubulointerstitial nephritis antigen. [refseq;acc:nm_014464]	1.68817	53	Low confidence	Squared	4.66624	Divided
			765			6.18923	Subtracted
7.90063	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	14.4058	25		Rooted	1.82337	Divided
			34			6.50517	Subtracted
			39	High confidence		1.82337	Divided
			67			6.50517	Subtracted
7.9671	nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505]	10.6057	90	Low confidence		1.33119	Divided
			309			2.6386	Subtracted
7.96876	nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8]	10.6064	91			1.331	Divided
			310			2.63764	Subtracted
8.0312	tubulointerstitial nephritis antigen. [refseq;acc:nm_014464]	7.85784	689			1.02206	Divided
			787			0.17336	Subtracted
8.05424	ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]	8.90701	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	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]	43.7473	49		Squared	5.39519	Divided
			351			35.6387	Subtracted
8.11997	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]	115.385	13	Low confidence	Measured	14.21	Divided
			423			107.265	Subtracted
8.12404	arf gtpase-activating protein. [refseq;acc:nm_133446]	6.08276	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	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]	6.488	112			1.25512	Divided
			436			1.65525	Subtracted
8.15919	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	4.74982	146	High confidence	Squared	1.71779	Divided
			424			3.40937	Subtracted
8.27667	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	5.86733	206			1.41064	Divided
			434			2.40934	Subtracted
8.27669	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	4.90793	149			1.68639	Divided
			425			3.36876	Subtracted
8.45575	pou domain, class 3, transcription factor 3 (brain-specific homeobox/pou domain protein 1) (brain-1) (brn-1 protein). [swissprot;acc:p20264]	8.33665	736	Low confidence	Rooted	1.01429	Divided
			802			0.1191	Subtracted
8.48528	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	12.2882	60	High confidence		1.44818	Divided
			63	Low confidence
			144	High confidence		3.80292	Subtracted
			225	Low confidence
8.52047	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]	10.0173	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	protein c20orf142 precursor. [swissprot;acc:q8n6m3]	9.74679	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.