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

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Showing element 1 to 32 of 32 in total

Rank  : 8

Filtered	green	network_comparison	Value Type	Network Comparison Type	red	Interaction Map	description
0	0.00001	159148	Squared	Divided	1.59148	High confidence	ero1-like. [refseq;acc:nm_014584]
		360555	Rooted		3.60555	Low confidence	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
		905539			9.05539	High confidence	ero1-like. [refseq;acc:nm_014584]
	43	4300000	Measured		0.00001		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
	56.7758	15.3379	Rooted	Subtracted	72.1137		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]
	111.067	15.292			126.359	Low confidence	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]
	6410	75.4118	Measured	Divided	85		ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]
	7500.75	2393.82		Subtracted	5106.93	High confidence	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]
	8770.72	1232.83			7537.89	Low confidence	zinc finger protein 277. [swissprot;acc:q9nrm2]
	13216	1.68629	Ranked	Divided	22286		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]
		9070		Subtracted		High confidence	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
	19295.9	11098	Squared	Divided	1.73869	Low confidence	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]
	19873	8983.6	Ranked	Subtracted	10889.4		ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]
	21888	1.89918		Divided	11525	High confidence	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]
	61843.5	16419.5	Squared	Subtracted	45424	Low confidence	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]
	386144	28560			414704	High confidence	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]
1	18.4255	1.84327	Rooted	Divided	33.9632		db83 protein. [swissprot;acc:p57088]
	27.2805	11.544	Squared		314.926
	45.9728	18.8343	Rooted	Subtracted	27.1385	Low confidence	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]
	47.6922	1.49674		Divided	31.8641		thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]
	168.796	23.245		Subtracted	145.551	High confidence	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]
	240	1.325	Ranked	Divided	318	Low confidence	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]
	247.246	58.226		Subtracted	305.472		thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]
	322	1.49767		Divided	215	High confidence	hbs1-like. [refseq;acc:nm_006620]
	339.5	3.39764	Measured		1153.5		db83 protein. [swissprot;acc:p57088]
	362	74	Ranked	Subtracted	288		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]
	5058.5	1.54317	Measured	Divided	3278	Low confidence	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]
	6056.43	2.38136	Squared		2543.26
	28492	7307	Measured	Subtracted	21185	High confidence	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]
	39358.1	6246.7			33111.4	Low confidence	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]
	192141	85915	Squared		106226		mitochondrial solute carrier protein. [refseq;acc:nm_145305]
	354894	104591			250303	High confidence	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]

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.