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

Results: HTML CSV LaTeX

Showing element 432 to 481 of 3228 in total

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

Rank	green	description	network_comparison	red
432	229.411	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]	1.07934	212.547
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	205.286	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	1.07909	221.522
436		paxillin. [swissprot;acc:p49023]
437	226.459	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	1.07878	209.921
438	216.674	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	1.07869	233.723
439	257.784	40s ribosomal protein s9. [swissprot;acc:p46781]	1.07866	238.986
440	249.983	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	1.07843	231.802
441	207.222	grb2-related adaptor protein. [swissprot;acc:q13588]	1.07835	223.457
442	207.55	e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	1.0783	223.802
443	207.539	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
444	207.549	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443]		223.801
445		neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]
446	207.785	growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354]	1.07827	224.049
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	246.338	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	1.07822	228.468
449	246.33	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]	1.07821	228.463
450	218.837	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	1.07815	235.94
451	257.705	polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468]	1.07785	239.092
452	207.972	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	1.07784	224.161
453		u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]
454	226.578	40s ribosomal protein s26. [swissprot;acc:p02383]	1.07779	210.224
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	218.925	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	1.07764	235.922
459	216.737	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]	1.07748	233.529
460	207.62	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	1.0772	223.648
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	236.224	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	1.07709	254.434
463	257.327	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9]	1.07704	238.921
464	226.764	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	1.07686	210.578
465	267.226	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]		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	209.651	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	1.07637	225.661
474	210.818	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389]	1.07576	226.789
475	210.816	potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470]	1.07547	226.727
476	210.814	potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459]	1.07527	226.681
477	234.547	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	1.0741	251.926
478	212.321	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994]	1.07409	228.051
479		nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]
480	254.667	neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092]	1.07405	237.109
481		neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]

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.