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

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Showing element 4014 to 4063 of 12912 in total

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

Rank	Value Type	description	red	green	network_comparison
1004	Ranked	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	238.725	231.059	1.03318
	Squared	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868]	17541.4	20148.6	1.14863
	Rooted	interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167]	61.5654	64.9046	1.05424
1005	Measured	annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073]	5780.34	6329.3	1.09497
	Ranked	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	225.448	218.232	1.03307
	Squared	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5]	17541.4	20148.6	1.14863
	Rooted	xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736]	64.9107	68.4287	1.0542
1006	Measured	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936]	5707.73	6249.1	1.09485
	Ranked	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	116.524	120.375	1.03305
	Squared	exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4]	17541.4	20148.6	1.14863
	Rooted	kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139]	59.3039	62.5177	1.05419
1007	Measured	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794]	5707.73	6249.1	1.09485
	Ranked	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	162.055	156.884	1.03296
	Squared	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	17603.1	20218.5	1.14858
	Rooted	pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687]	64.0132	67.4724	1.05404
1008	Measured	single-minded homolog 1. [swissprot;acc:p81133]	5707.73	6249.1	1.09485
	Ranked	wd-repeat protein bing4. [swissprot;acc:o15213]	243.227	235.475	1.03292
	Squared	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]	17603.1	20218.5	1.14858
	Rooted	eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613]	51.2693	54.0336	1.05392
1009	Measured	synapsin iii. [swissprot;acc:o14994]	5791.82	6340.86	1.0948
	Ranked	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	229.116	221.823	1.03288
	Squared	40s ribosomal protein s24 (s19). [swissprot;acc:p16632]	21492.5	24677.4	1.14819
	Rooted	exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400]	58.8768	62.0483	1.05387
1010	Measured	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	5791.82	6340.86	1.0948
	Ranked	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	217.523	210.648	1.03264
	Squared	proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332]	24025.9	27585.7	1.14817
	Rooted	nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231]	62.0618	65.4025	1.05383
1011	Measured	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]	5791.82	6340.86	1.0948
	Ranked	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	217.026	210.189	1.03253
	Squared	molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007]	24025.9	27585.7	1.14817
	Rooted	elks protein. [refseq;acc:nm_015064]	62.0618	65.4025	1.05383
1012	Measured	actin binding lim protein 2. [refseq;acc:nm_032432]	5791.82	6340.86	1.0948
	Ranked	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	217.021	210.185	1.03252
	Squared	anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885]	24025.9	27585.7	1.14817
	Rooted	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530]	74.9231	78.9471	1.05371
1013	Measured	hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571]	5791.82	6340.86	1.0948
	Ranked	protein bap28. [swissprot;acc:q9h583]	244.312	236.647	1.03239
	Squared	60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914]	24025.9	27585.7	1.14817
	Rooted	heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849]	58.0289	61.136	1.05354
1014	Measured	synapsin ii. [swissprot;acc:q92777]	5791.82	6340.86	1.0948
	Ranked	apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]	243.045	235.422	1.03238
	Squared	proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591]	24025.9	27585.7	1.14817
	Rooted	n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784]	58.0289	61.136	1.05354
1015	Measured	mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]	5791.82	6340.86	1.0948
	Ranked	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742]	221.73	228.906	1.03236
	Squared	molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396]	24025.9	27585.7	1.14817
	Rooted	n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569]	58.0289	61.136	1.05354
1016	Measured	peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542]	5791.82	6340.86	1.0948
	Ranked	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629]	217.369	210.561	1.03233
	Squared	eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613]	15559.9	17865	1.14814

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.