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 5080 to 5129 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
2540	toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603]	Divided	217.144	216.699	1.00205
2541	aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868]		194.505	194.902	1.00204
	chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197]	Subtracted	188.228	188.63	0.402
2542	epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964]		217.587	217.988	0.401
	p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162]	Divided	218.068	217.633	1.002
2543	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	190.765	191.163	0.398
	tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7]	Divided	224.726	225.164	1.00195
2544	aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728]		212.67	212.262	1.00192
	aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868]	Subtracted	194.505	194.902	0.397
2545	elongation factor 2 (ef-2). [swissprot;acc:p13639]		222.658	223.047	0.389
	proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065]	Divided	213.494	213.088	1.00191
2546	metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416]	Subtracted	222.658	223.047	0.389
	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975]	Divided	197.138	197.507	1.00187
2547	glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410]		206.894	206.51	1.00186
	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	Subtracted	222.658	223.047	0.389
2548	glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409]	Divided	206.899	206.516	1.00185
	glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410]	Subtracted	206.894	206.51	0.384
2549	glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189]	Divided	206.902	206.519	1.00185
	glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409]	Subtracted	206.899	206.516	0.383
2550	epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964]	Divided	217.587	217.988	1.00184
	glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189]	Subtracted	206.902	206.519	0.383
2551	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	Divided	209.766	210.148	1.00182
		Subtracted			0.382
2552	s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153]		212.953	212.572	0.381
	testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8]	Divided	193.12	193.467	1.0018
2553	44050 protein. [refseq;acc:nm_178832]	Subtracted	151.386	151.009	0.377
	chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824]	Divided	193.12	193.467	1.0018
2554	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]	Subtracted	151.386	151.009	0.377
	testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7]	Divided	193.12	193.467	1.0018
2555	s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153]		212.953	212.572	1.00179
	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975]	Subtracted	197.138	197.507	0.369
2556	chromodomain y-like protein 2. [refseq;acc:nm_152342]	Divided	193.119	193.46	1.00177
	serine/threonine protein kinase 12 (ec 2.7.1.37) (aurora- and ipl1- like midbody-associated protein 1) (aim-1) (aurora/ipl1-related kinase 2) (aurora-related kinase 2) (stk-1) (aurora-b). [swissprot;acc:q96gd4]	Subtracted	219.907	220.267	0.36
2557	elongation factor 2 (ef-2). [swissprot;acc:p13639]	Divided	222.658	223.047	1.00175
	kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241]	Subtracted	219.907	220.267	0.36
2558	metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416]	Divided	222.658	223.047	1.00175
	serine/threonine protein kinase 13 (ec 2.7.1.37) (aurora/ipl1/eg2 protein 2) (aurora/ipl1-related kinase 3) (aurora-c). [swissprot;acc:q9uqb9]	Subtracted	219.907	220.267	0.36
2559	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	Divided	222.658	223.047	1.00175
	serine/threonine kinase 6 (ec 2.7.1.37) (serine/threonine kinase 15) (aurora/ipl1-related kinase 1) (aurora-related kinase 1) (hark1) (aurora-a) (breast-tumor-amplified kinase). [swissprot;acc:o14965]	Subtracted	219.907	220.267	0.36
2560	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]
	monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283]	Divided	202.395	202.042	1.00175
2561	fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467]		209.825	210.18	1.00169
		Subtracted			0.355
2562	glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976]	Divided	208.429	208.779	1.00168
	monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283]	Subtracted	202.395	202.042	0.353
2563	adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [swissprot;acc:p55263]	Divided	208.429	208.779	1.00168
	glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976]	Subtracted			0.35
2564	adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [swissprot;acc:p55263]
	protein x 0001. [refseq;acc:nm_016302]	Divided			1.00168
2565	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]

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.