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

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Showing element 1 to 32 of 32 in total

Rank  : 8

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

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.