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 877 to 926 of 3730 in total

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

Rank	description	Filtered	red	green	network_comparison
439	40s ribosomal protein s9. [swissprot;acc:p46781]	1	238.986	257.784	1.07866
	histone h2b. [refseq;acc:nm_175055]	0	8770.3	8574.79	1.0228
440	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	1	231.802	249.983	1.07843
	histone h2b.e (h2b/e). [swissprot;acc:q99879]	0	8770.28	8574.81	1.0228
441	grb2-related adaptor protein. [swissprot;acc:q13588]	1	223.457	207.222	1.07835
	histone h2b.c (h2b/c). [swissprot;acc:q99880]	0	8770.14	8574.98	1.02276
442	e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	1	223.802	207.55	1.0783
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	0	14570.4	14247.3	1.02268
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]	1	223.79	207.539	1.0783
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	0	9141.6	8940.14	1.02253
444	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]		14556.7	14237.8	1.0224
	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443]	1	223.801	207.549	1.0783
445	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	0	7965.06	7790.78	1.02237
	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]	1	223.801	207.549	1.0783
446	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	0	7965.06	7790.78	1.02237
	growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354]	1	224.049	207.785	1.07827
447	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	0	12532.2	12808.8	1.02207
	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]	1	224.049	207.785	1.07827
448	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]		228.468	246.338	1.07822
	protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284]	0	2939	2876	1.02191
449	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]		9897.12	9690.83	1.02129
	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	228.463	246.33	1.07821
450	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]		235.94	218.837	1.07815
	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	0	11290.8	11525.8	1.02081
451	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]		14010.2	13737.2	1.01987
	polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468]	1	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
	neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004]	0	14010.2	13737.2	1.01987
453	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594]
	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]	1	224.161	207.972	1.07784
454	40s ribosomal protein s26. [swissprot;acc:p02383]		210.224	226.578	1.07779
	lats homolog 1. [refseq;acc:nm_004690]	0	13933.5	14204.8	1.01947
455	mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584]	1	210.225	226.578	1.07779
	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	0	13933.5	14204.8	1.01947
456	atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]	1	210.225	226.578	1.07779
	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	0	16416.1	16721.6	1.01861
457	ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927]	1	210.225	226.578	1.07779
	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]	0	16416.1	16721.6	1.01861
458	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	1	235.922	218.925	1.07764
	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]	0	16416.1	16721.6	1.01861
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]	1	233.529	216.737	1.07748
	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]	0	20875	20495	1.01854
460	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]		20914	20558	1.01732
	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	1	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]
	scratch; scratch 1. [refseq;acc:nm_031309]	0	12164.9	12358.1	1.01588
462	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]		12189.6	12378.3	1.01548
	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	1	254.434	236.224	1.07709
463	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	0	5558.06	5473.99	1.01536
	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9]	1	238.921	257.327	1.07704

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.