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

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Showing element 1180 to 1229 of 3228 in total

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

red	Rank	green	description	network_comparison
5117.85	1445	5510.45	cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493]	1.07671
	1446		peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526]
	1447		iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413]
5123.89	2334	5350.78	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	1.04428
	2335		microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005]
	2336		uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172]
	2337		cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]
	2338		bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213]
	2339		phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058]
5132.68	1231	5569.54	probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2]	1.08511
5136.78	120	6895.98	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]	1.34247
5140.14	122	6893.53	high-mobility group 20a. [refseq;acc:nm_018200]	1.34112
5144.74	997	5634	nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838]	1.0951
	998		transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269]
5147.9	990	5641.25	dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0]	1.09584
5148.71	611	5811.74	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	1.12878
5148.88	2262	5386.34	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]	1.04612
5150.14	2260	5387.84	block 23. [sptrembl;acc:q8nhw5]	1.04615
5150.31	2258	5388.05	60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388]	1.04616
5162.27	1570	5534.71	n-acetylglutamate synthase. [refseq;acc:nm_153006]	1.07215
5162.52	617	5822.47	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	1.12783
5166.04	880	5694.55	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	1.1023
5167.15	884	5695.44	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	1.10224
5167.88	647	4594.43	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	1.12481
5168.01	885	5696.12	mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]	1.10219
5168.43	651	4597.44	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	1.1242
	652		short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]
5171.45	1936	5486.96	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	1.06101
	1937		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]
	1938		williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]
5172.07	827	5723.22	transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403]	1.10656
5176.92	2695	5154.43	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]	1.00436
	2696		programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831]
	2697		t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]
5181.2	234	6410.58	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	1.23728
	235		ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]
5184.45	1599	5554.97	40s ribosomal protein s24 (s19). [swissprot;acc:p16632]	1.07147
5184.94	1594	5555.76	transportin-sr; importin 12. [refseq;acc:nm_012470]	1.07152
5189	364	6088.47	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	1.17334
	365		calcyphosine. [swissprot;acc:q13938]
	366		crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]
5195.3	1955	5510.67	28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3]	1.0607
5195.48	842	5741.63	loh1cr12. [refseq;acc:nm_058169]	1.10512
	843		unr protein. [swissprot;acc:o75534]
5195.58	826	5750.34	exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400]	1.10678
5201.41	399	4479.76	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	1.16109
	400		adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]
	401		adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]
	402		leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]
	403		fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]

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.