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	green	red	network_comparison

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Showing element 425 to 474 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	green	red	network_comparison
425	max protein. [swissprot;acc:p25912]	210.561	227.828	1.082
426	dynactin 4. [refseq;acc:nm_032486]	252.253	233.142	1.08197
427	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	259.525	239.977	1.08146
428	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	234.808	253.852	1.0811
429	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	259.038	239.709	1.08064
430	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	210.888	227.748	1.07995
431	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	255.113	236.245	1.07987
432	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]	229.411	212.547	1.07934
433	programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831]
434	t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]
435	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	205.286	221.522	1.07909
436	paxillin. [swissprot;acc:p49023]
437	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	226.459	209.921	1.07878
438	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	216.674	233.723	1.07869
439	40s ribosomal protein s9. [swissprot;acc:p46781]	257.784	238.986	1.07866
440	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	249.983	231.802	1.07843
441	grb2-related adaptor protein. [swissprot;acc:q13588]	207.222	223.457	1.07835
442	e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	207.55	223.802	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]	207.539	223.79
444	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443]	207.549	223.801
445	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]
446	growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354]	207.785	224.049	1.07827
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]
448	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	246.338	228.468	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]	246.33	228.463	1.07821
450	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	218.837	235.94	1.07815
451	polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468]	257.705	239.092	1.07785
452	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	207.972	224.161	1.07784
453	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]
454	40s ribosomal protein s26. [swissprot;acc:p02383]	226.578	210.224	1.07779
455	mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584]		210.225
456	atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]
457	ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927]
458	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	218.925	235.922	1.07764
459	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]	216.737	233.529	1.07748
460	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	207.62	223.648	1.0772
461	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887]
462	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	236.224	254.434	1.07709
463	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9]	257.327	238.921	1.07704
464	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	226.764	210.578	1.07686
465	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	267.226	248.152
466	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]
467	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]
468	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]
469	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]
470	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]
471	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]
472	thymic stromal co-transporter. [refseq;acc:nm_033051]
473	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	209.651	225.661	1.07637
474	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389]	210.818	226.789	1.07576

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.