Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

Results: HTML CSV LaTeX

Showing element 418 to 467 of 3228 in total

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

Rank	description	network_comparison	green	red	
418	cd209 antigen-like; putative type ii membrane protein. [source:refseq;acc:nm_014257]	1.08417	253.197	233.539	
419	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [source:swissprot;acc:p06734]	1.08417	253.197	233.539	
420	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [source:refseq;acc:nm_021155]	1.08417	253.197	233.539	
421	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	1.08403	205.9	223.202	
422	ras-related protein rab-37. [source:swissprot;acc:q96ax2]	1.08284	260.193	240.287	
423	ras-related protein rab-26. [source:swissprot;acc:q9ulw5]	1.08284	260.193	240.287	
424	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [source:swissprot;acc:p19387]	1.08284	260.193	240.287	
425	max protein. [source:swissprot;acc:p25912]	1.082	210.561	227.828	
426	dynactin 4. [source:refseq;acc:nm_032486]	1.08197	252.253	233.142	
427	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [source:swissprot;acc:p19388]	1.08146	259.525	239.977	
428	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [source:refseq;acc:nm_024072]	1.0811	234.808	253.852	
429	polymerase (rna) iii (dna directed) (32kd). [source:refseq;acc:nm_006467]	1.08064	259.038	239.709	
430	u6 snrna-associated sm-like protein lsm5. [source:swissprot;acc:q9y4y9]	1.07995	210.888	227.748	
431	trub pseudouridine (psi) synthase homolog 1. [source:refseq;acc:nm_139169]	1.07987	255.113	236.245	
432	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [source:swissprot;acc:q14249]	1.07934	229.411	212.547	
433	programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [source:swissprot;acc:o95831]	1.07934	229.411	212.547	
434	t-box transcription factor tbx6 (t-box protein 6). [source:swissprot;acc:o95947]	1.07934	229.411	212.547	
435	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [source:refseq;acc:nm_007195]	1.07909	205.286	221.522	
436	paxillin. [source:swissprot;acc:p49023]	1.07909	205.286	221.522	
437	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [source:swissprot;acc:q15642]	1.07878	226.459	209.921	
438	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [source:swissprot;acc:p41227]	1.07869	216.674	233.723	
439	40s ribosomal protein s9. [source:swissprot;acc:p46781]	1.07866	257.784	238.986	
440	highly expressed in cancer, rich in leucine heptad repeats. [source:refseq;acc:nm_006101]	1.07843	249.983	231.802	
441	grb2-related adaptor protein. [source:swissprot;acc:q13588]	1.07835	207.222	223.457	
442	e2a-pbx1-associated protein; putative 47 kda protein. [source:refseq;acc:nm_020140]	1.0783	207.55	223.802	
443	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [source:refseq;acc:nm_145117]	1.0783	207.539	223.79	
444	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [source:refseq;acc:nm_020443]	1.0783	207.549	223.801	
445	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [source:refseq;acc:nm_014903]	1.0783	207.549	223.801	
446	growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [source:swissprot;acc:p29354]	1.07827	207.785	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). [source:swissprot;acc:p51955]	1.07827	207.785	224.049	
448	microtubule-actin crosslinking factor 1, isoform 4. [source:swissprot;acc:q96pk2]	1.07822	246.338	228.468	
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). [source:swissprot;acc:q03001]	1.07821	246.33	228.463	
450	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	1.07815	218.837	235.94	
451	polymerase (rna) iii (dna directed) (62kd). [source:refseq;acc:nm_006468]	1.07785	257.705	239.092	
452	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36]	1.07784	207.972	224.161	
453	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [source:swissprot;acc:p09661]	1.07784	207.972	224.161	
454	40s ribosomal protein s26. [source:swissprot;acc:p02383]	1.07779	226.578	210.224	
455	mitochondrial import inner membrane translocase subunit tim22. [source:swissprot;acc:q9y584]	1.07779	226.578	210.225	
456	atp synthase mitochondrial f1 complex assembly factor 2. [source:refseq;acc:nm_145691]	1.07779	226.578	210.225	
457	ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [source:swissprot;acc:p14927]	1.07779	226.578	210.225	
458	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	1.07764	218.925	235.922	
459	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [source:swissprot;acc:o95817]	1.07748	216.737	233.529	
460	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [source:swissprot;acc:q15428]	1.0772	207.62	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). [source:swissprot;acc:q13887]	1.0772	207.62	223.648	
462	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [source:refseq;acc:nm_032390]	1.07709	236.224	254.434	
463	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [source:swissprot;acc:q9h1d9]	1.07704	257.327	238.921	
464	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [source:sptrembl;acc:q96lh6]	1.07686	226.764	210.578	
465	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	1.07686	267.226	248.152	
466	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306]	1.07686	267.226	248.152	
467	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [source:swissprot;acc:o95622]	1.07686	267.226	248.152	

Legend:
- Rank is the rank after comparing the two networks
- 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.

- http://analysis.yellowcouch.org/