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	Hugo	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 430 to 479 of 3228 in total

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

Rank	description	Hugo	red	green	network_comparison
430	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	LSM5	227.748	210.888	1.07995
431	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	TRUB1	236.245	255.113	1.07987
432	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]	ENDOG	212.547	229.411	1.07934
433	programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831]	AIFM1
434	t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]	TBX6
435	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	POLI	221.522	205.286	1.07909
436	paxillin. [swissprot;acc:p49023]	PXN
437	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	TRIP10	209.921	226.459	1.07878
438	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	ARD1A	233.723	216.674	1.07869
439	40s ribosomal protein s9. [swissprot;acc:p46781]	RPS9	238.986	257.784	1.07866
440	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	NDC80	231.802	249.983	1.07843
441	grb2-related adaptor protein. [swissprot;acc:q13588]	GRAP	223.457	207.222	1.07835
442	e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	ANKS1B	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]	NAV2	223.79	207.539
444	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443]	NAV1	223.801	207.549
445	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]	NAV3
446	growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354]	GRB2	224.049	207.785	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]	NEK2
448	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	MACF1	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]	DST	228.463	246.33	1.07821
450	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	SRP9	235.94	218.837	1.07815
451	polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468]	POLR3C	239.092	257.705	1.07785
452	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	no value	224.161	207.972	1.07784
453	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]	SNRPA1
454	40s ribosomal protein s26. [swissprot;acc:p02383]	no value	210.224	226.578	1.07779
455	mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584]	TIMM22	210.225
456	atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]	ATPAF2
457	ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927]	UQCRB
458	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	SRP9	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]	BAG3	233.529	216.737	1.07748
460	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	SF3A2	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]	KLF5
462	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	MKI67IP	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]	POLR3F	238.921	257.327	1.07704
464	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	FNBP1	210.578	226.764	1.07686
465	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	CHRNA7	248.152	267.226
466	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]	ADCY6
467	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	ADCY5
468	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	LRRC15
469	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]	FEM1B
470	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	LRRC3
471	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]	LAMC1
472	thymic stromal co-transporter. [refseq;acc:nm_033051]	SLC46A2
473	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	PRPF31	225.661	209.651	1.07637
474	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389]	KCNA2	226.789	210.818	1.07576
475	potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470]	KCNA1	226.727	210.816	1.07547
476	potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459]	KCNA4	226.681	210.814	1.07527
477	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	NIP7	251.926	234.547	1.0741
478	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]	BRF1	228.051	212.321	1.07409
479	nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]	NOLA1

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
- Hugo is the HGNC identifier if it exists
- 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.