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 2630 to 2679 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
658	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	Ranked	229.072	216.576	1.0577
	eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884]	Rooted	52.7523	56.8686	1.07803
	similar to trna synthetase class ii. [refseq;acc:nm_152268]	Squared	22293.8	26242.6	1.17713
659	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	Rooted	51.7081	47.9816	1.07767
	hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3]	Ranked	229.072	216.576	1.0577
	ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480]	Squared	24614	28973.4	1.17711
	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Measured	6089.21	6835.34	1.12253
660	actin binding lim protein 2. [refseq;acc:nm_032432]	Ranked	229.072	216.576	1.0577
	fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917]	Rooted	133.216	123.627	1.07756
	nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9]	Squared	33024.9	38867.8	1.17692
	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	Measured	5575.18	6254.85	1.12191
661	delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716]	Squared	22223.1	26152.4	1.17681
	hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571]	Ranked	229.072	216.576	1.0577
	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	Rooted	68.8243	74.1496	1.07738
	step ii splicing factor slu7. [refseq;acc:nm_006425]	Measured	5575.18	6254.85	1.12191
662	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5]	Rooted	68.8237	74.1484	1.07737
	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4]	Measured	6374.65	7145.59	1.12094
	synapsin ii. [swissprot;acc:q92777]	Ranked	229.072	216.576	1.0577
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Squared	23947.4	28163.7	1.17607
663	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]		23947.7	28163.9	1.17606
	mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]	Ranked	229.072	216.576	1.0577
	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9]	Rooted	68.8197	74.1413	1.07733
	tubby protein homolog. [swissprot;acc:p50607]	Measured	6374.65	7145.59	1.12094
664	neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863]	Rooted	51.6042	55.574	1.07693
	peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542]	Ranked	229.072	216.576	1.0577
	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743]	Measured	6374.65	7145.59	1.12094
	ubiquitin-like protein smt3a. [swissprot;acc:p55854]	Squared	23948	28164.1	1.17605
665	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259]	Ranked	229.072	216.576	1.0577
	numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]	Measured	6374.65	7145.59	1.12094
	rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555]	Rooted	51.6042	55.574	1.07693
	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	Squared	18960.3	22298	1.17604
666	down-regulated in metastasis. [refseq;acc:nm_014503]	Rooted	51.6042	55.574	1.07693
	glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057]	Squared	29224	34362.1	1.17582
	tbc1 domain family member 5. [swissprot;acc:q92609]	Measured	6374.65	7145.59	1.12094
	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469]	Ranked	229.072	216.576	1.0577
667	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
	proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272]	Squared	29224	34362.1	1.17582
	tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]	Measured	6374.65	7145.59	1.12094
	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	Rooted	51.2483	47.5889	1.0769
668	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]	Ranked	229.072	216.576	1.0577
	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	Rooted	95.4476	102.785	1.07687
	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	Squared	23969.3	28175.3	1.17547
	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]	Measured	6374.65	7145.59	1.12094
669	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	Rooted	79.931	86.0693	1.07679
	numb-like protein (numb-r). [swissprot;acc:q9y6r0]	Measured	6374.65	7145.59	1.12094
	synapsin i (brain protein 4.1). [swissprot;acc:p17600]	Ranked	229.072	216.576	1.0577
	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0]	Squared	18548.7	21798.2	1.17519
670	autoantigen ngp-1. [swissprot;acc:q13823]	Ranked	250.302	236.817	1.05694
	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]	Rooted	51.2122	47.5637	1.07671
	dok-like protein. [refseq;acc:nm_024872]	Squared	28911	33971.3	1.17503

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.