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 851 to 900 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
426	dynactin 4. [refseq;acc:nm_032486]	Divided	233.142	252.253	1.08197
	programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831]	Subtracted	212.547	229.411	16.864
427	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	Divided	239.977	259.525	1.08146
	t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]	Subtracted	212.547	229.411	16.864
428	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	Divided	253.852	234.808	1.0811
	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	Subtracted	227.748	210.888	16.86
429	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	Divided	239.709	259.038	1.08064
	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	Subtracted	251.344	234.514	16.83
430	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]		250.938	234.134	16.804
	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	Divided	227.748	210.888	1.07995
431	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817]	Subtracted	233.529	216.737	16.792
	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	Divided	236.245	255.113	1.07987
432	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]		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

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.