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

Results: HTML CSV LaTeX

Showing element 2001 to 2050 of 6456 in total

Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
1001	lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571]	Divided	5680.76	6220.45	1.095
	splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246]	Subtracted	10178.5	9638.08	540.42
1002	seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81]	Divided	5680.76	6220.45	1.095
	triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098]	Subtracted			539.69
1003	ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2]
	seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591]	Divided			1.095
1004	lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571]	Subtracted			539.69
	o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807]	Divided	5391.64	5903.72	1.09498
1005	annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073]		5780.34	6329.3	1.09497
	seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81]	Subtracted	5680.76	6220.45	539.69
1006	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936]	Divided	5707.73	6249.1	1.09485
	seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591]	Subtracted	5680.76	6220.45	539.69
1007	cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238]		5706.5	6245.55	539.05
	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794]	Divided	5707.73	6249.1	1.09485
1008	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	Subtracted	2554.89	3093.78	538.89
	single-minded homolog 1. [swissprot;acc:p81133]	Divided	5707.73	6249.1	1.09485
1009	heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849]	Subtracted	5210.58	5749.33	538.75
	synapsin iii. [swissprot;acc:o14994]	Divided	5791.82	6340.86	1.0948
1010	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
	n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784]	Subtracted	5210.58	5749.33	538.75
1011	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]	Divided	5791.82	6340.86	1.0948
	n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569]	Subtracted	5210.58	5749.33	538.75
1012	actin binding lim protein 2. [refseq;acc:nm_032432]	Divided	5791.82	6340.86	1.0948
	heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [swissprot;acc:p52848]	Subtracted	5210.58	5749.33	538.75
1013	hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571]	Divided	5791.82	6340.86	1.0948
	protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260]	Subtracted	5210.58	5749.33	538.75
1014	synapsin ii. [swissprot;acc:q92777]	Divided	5791.82	6340.86	1.0948
	uridine kinase-like 1. [swissprot;acc:q9nwz5]	Subtracted	5548.78	6086.89	538.11
1015	acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763]		7237.39	7775.21	537.82
	mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]	Divided	5791.82	6340.86	1.0948
1016	peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542]
	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749]	Subtracted	3889.27	4426.74	537.47
1017	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259]	Divided	5791.82	6340.86	1.0948
	rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243]	Subtracted	3889.27	4426.74	537.47
1018	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751]
	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469]	Divided	5791.82	6340.86	1.0948
1019	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
	nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274]	Subtracted	5704	6241.36	537.36
1020	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]	Divided	5791.82	6340.86	1.0948
	serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743]	Subtracted	7234.61	7771.58	536.97
1021	sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312]
	synapsin i (brain protein 4.1). [swissprot;acc:p17600]	Divided	5791.82	6340.86	1.0948
1022	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760]		6435.94	7045.75	1.09475
	tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801]	Subtracted	6783.78	7320.39	536.61
1023	acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085]		7232.14	7768.35	536.21
	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761]	Divided	6435.02	7044.65	1.09474
1024	cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238]		5706.5	6245.55	1.09446
	topoisomerase-related function protein 4-2. [refseq;acc:nm_022447]	Subtracted	4725.28	5261.06	535.78
1025	nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570]		5947.53	6481.56	534.03
	phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305]	Divided	5511.96	6031.95	1.09434

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.