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

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Showing element 863 to 912 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
432	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]	Divided	212.547	229.411	1.07934
	mct-1 protein. [refseq;acc:nm_014060]	Subtracted	226.313	243.03	16.717
433	mitochondrial ribosomal protein l22. [refseq;acc:nm_014180]
	programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831]	Divided	212.547	229.411	1.07934
434	ad24 protein. [refseq;acc:nm_022451]	Subtracted	251.334	234.672	16.662
	t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]	Divided	212.547	229.411	1.07934
435	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]		221.522	205.286	1.07909
	wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7]	Subtracted	251.299	234.729	16.57
436	paxillin. [swissprot;acc:p49023]	Divided	221.522	205.286	1.07909
	triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938]	Subtracted	231.496	248.048	16.552
437	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	Divided	209.921	226.459	1.07878
		Subtracted			16.538
438	block of proliferation 1. [swissprot;acc:q14137]		250.794	234.433	16.361
	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	Divided	233.723	216.674	1.07869
439	40s ribosomal protein s9. [swissprot;acc:p46781]		238.986	257.784	1.07866
	pescadillo homolog 1. [swissprot;acc:o00541]	Subtracted	251.297	234.941	16.356
440	40s ribosomal protein s26. [swissprot;acc:p02383]		210.224	226.578	16.354
	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	Divided	231.802	249.983	1.07843
441	grb2-related adaptor protein. [swissprot;acc:q13588]		223.457	207.222	1.07835
	mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584]	Subtracted	210.225	226.578	16.353
442	atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]
	e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	Divided	223.802	207.55	1.0783
443	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117]		223.79	207.539
	ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927]	Subtracted	210.225	226.578	16.353
444	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443]	Divided	223.801	207.549	1.0783
	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	Subtracted	250.053	233.725	16.328
445	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]	Divided	223.801	207.549	1.0783
	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	Subtracted	250.858	234.563	16.295
446	growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354]	Divided	224.049	207.785	1.07827
		Subtracted			16.264
447	serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955]	Divided			1.07827
		Subtracted			16.264
448	e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]		223.802	207.55	16.252
	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	Divided	228.468	246.338	1.07822
449	bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001]		228.463	246.33	1.07821
	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443]	Subtracted	223.801	207.549	16.252
450	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Divided	235.94	218.837	1.07815
451	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117]	Subtracted	223.79	207.539	16.251
	polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468]	Divided	239.092	257.705	1.07785
452	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]		224.161	207.972	1.07784
	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	Subtracted	221.522	205.286	16.236
453	paxillin. [swissprot;acc:p49023]
	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]	Divided	224.161	207.972	1.07784
454	40s ribosomal protein s26. [swissprot;acc:p02383]		210.224	226.578	1.07779
	grb2-related adaptor protein. [swissprot;acc:q13588]	Subtracted	223.457	207.222	16.235
455	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]		224.161	207.972	16.189
	mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584]	Divided	210.225	226.578	1.07779
456	atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]
	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]	Subtracted	224.161	207.972	16.189

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.