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 918 to 967 of 3730 in total

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

Rank	description	Filtered	red	green	network_comparison
459	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
464	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]		210.578	226.764	1.07686
	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	0	10076.4	9928.08	1.01494
465	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	1	248.152	267.226	1.07686
	transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724]	0	9482.68	9620.66	1.01455
466	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]	1	248.152	267.226	1.07686
	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	0	1543	1521	1.01446
467	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	1	248.152	267.226	1.07686
	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	0	21205	20914	1.01391
468	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	1	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]
	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]	0	21205	20914	1.01391
470	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	1	248.152	267.226	1.07686
471	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	0	11319.2	11463	1.0127
	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]	1	248.152	267.226	1.07686
472	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753]	0	7080.27	7165.6	1.01205
	thymic stromal co-transporter. [refseq;acc:nm_033051]	1	248.152	267.226	1.07686
473	cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098]	0	816	825	1.01103
	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	1	225.661	209.651	1.07637
474	lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]	0	11290.1	11167.6	1.01097
	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389]	1	226.789	210.818	1.07576
475	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	0	18667	18500	1.00903
	potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470]	1	226.727	210.816	1.07547
476	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	0	8403	8329	1.00888
	potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459]	1	226.681	210.814	1.07527
477	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]		251.926	234.547	1.0741
	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986]	0	15920	15780.2	1.00886
478	3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110]		10156.4	10243.1	1.00854
	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]	1	228.051	212.321	1.07409
479	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	0	15155.8	15031.7	1.00826
	nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]	1	228.051	212.321	1.07409
480	neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092]		237.109	254.667	1.07405
	uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]	0	15155.8	15031.7	1.00826
481	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]	1	237.109	254.667	1.07405
	uridine kinase-like 1. [swissprot;acc:q9nwz5]	0	11554.3	11462.4	1.00802
482	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839]	1	237.109	254.667	1.07405
	kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]	0	6156.33	6205.67	1.00801
483	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950]	1	237.109	254.667	1.07405
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	0	12223.8	12127.5	1.00794
484	e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]	1	237.109	254.667	1.07405

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.