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 412 to 461 of 3228 in total

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

Rank	description	red	green	network_comparison
412	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	240.788	261.416	1.08567
413	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]	240.913	261.45	1.08525
414	katanin p60 subunit a 1. [refseq;acc:nm_007044]	232.431	252.238	1.08522
415	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	232.382	252.166	1.08514
416	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6]	240.6	261.041	1.08496
417	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	233.539	253.197	1.08417
418	cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]
419	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]
420	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]
421	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	223.202	205.9	1.08403
422	ras-related protein rab-37. [swissprot;acc:q96ax2]	240.287	260.193	1.08284
423	ras-related protein rab-26. [swissprot;acc:q9ulw5]
424	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]
425	max protein. [swissprot;acc:p25912]	227.828	210.561	1.082
426	dynactin 4. [refseq;acc:nm_032486]	233.142	252.253	1.08197
427	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	239.977	259.525	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]	253.852	234.808	1.0811
429	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	239.709	259.038	1.08064
430	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	227.748	210.888	1.07995
431	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	236.245	255.113	1.07987
432	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]	212.547	229.411	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]	221.522	205.286	1.07909
436	paxillin. [swissprot;acc:p49023]
437	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	209.921	226.459	1.07878
438	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	233.723	216.674	1.07869
439	40s ribosomal protein s9. [swissprot;acc:p46781]	238.986	257.784	1.07866
440	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	231.802	249.983	1.07843
441	grb2-related adaptor protein. [swissprot;acc:q13588]	223.457	207.222	1.07835
442	e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	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]	223.79	207.539
444	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443]	223.801	207.549
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]	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]
448	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	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]	228.463	246.33	1.07821
450	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	235.94	218.837	1.07815
451	polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468]	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
453	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]
454	40s ribosomal protein s26. [swissprot;acc:p02383]	210.224	226.578	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]	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
460	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	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]

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.