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 901 to 950 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
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
457	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]		210.578	226.764	16.186
	ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927]	Divided	210.225	226.578	1.07779
458	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	Subtracted	251.653	235.506	16.147
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Divided	235.922	218.925	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]		233.529	216.737	1.07748
	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	Subtracted	250.538	234.401	16.137
460	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]		186.52	170.42	16.1
	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	Divided	223.648	207.62	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]
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Subtracted	186.52	170.42	16.1
462	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434]		236.662	252.708	16.046
	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	Divided	254.434	236.224	1.07709
463	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9]		238.921	257.327	1.07704
	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	Subtracted	223.648	207.62	16.028
464	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	Divided	210.578	226.764	1.07686
	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]	Subtracted	223.648	207.62	16.028
465	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564]		224.662	240.673	16.011
	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	Divided	248.152	267.226	1.07686
466	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]
	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	Subtracted	225.661	209.651	16.01
467	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	Divided	248.152	267.226	1.07686
	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	Subtracted	248.56	232.579	15.981
468	dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436]		237.627	253.604	15.977
	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	Divided	248.152	267.226	1.07686
469	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]
	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389]	Subtracted	226.789	210.818	15.971
470	inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537]		224.535	240.476	15.941
	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	Divided	248.152	267.226	1.07686
471	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]
	zinc finger-like protein 9. [refseq;acc:nm_033414]	Subtracted	250.942	235.004	15.938
472	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]
	thymic stromal co-transporter. [refseq;acc:nm_033051]	Divided	248.152	267.226	1.07686
473	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915]	Subtracted	250.942	235.004	15.938
	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	Divided	225.661	209.651	1.07637
474	potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470]	Subtracted	226.727	210.816	15.911
	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389]	Divided	226.789	210.818	1.07576
475	potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470]		226.727	210.816	1.07547
	protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316]	Subtracted	236.964	252.86	15.896

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.