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

Results: HTML CSV LaTeX

Showing element 2632 to 2681 of 14920 in total

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

description	Rank	Value Type	red	network_comparison	green
centromere/kinetochore protein zw10 homolog. [swissprot;acc:o43264]	3167	Rooted	0.00001	1	0.00001
cerebral cell adhesion molecule. [refseq;acc:nm_016174]	1234	Squared	62198.5	1.13507	70599.4
	1747	Measured	9596.59	1.06724	10241.9
	1837	Rooted	77.9868	1.03028	80.3483
	2508	Ranked	194.349	1.00247	193.871
cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	172		174.667	1.17685	205.556
	347	Rooted	66.4284	1.10713	60.0004
	900	Measured	4713.58	1.10152	4279.17
	2285	Squared	8157.62	1.07882	8800.59
cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]	384	Measured	4533.74	1.16447	5279.4
	493	Rooted	55.1759	1.09218	60.2621
	832	Ranked	231.734	1.0428	222.222
	885	Squared	18178.2	1.15974	21081.9
cgthba protein (-14 gene protein). [swissprot;acc:q12980]	644	Ranked	217.67	1.05938	230.596
	1360	Rooted	60.4911	1.04088	58.1154
	2562	Measured	5291.65	1.02002	5187.78
	2694	Squared	22249	1.02285	22757.3
channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700]	2078	Rooted	62.3035	1.02603	63.9253
	2085	Measured	5835.4	1.05552	6159.4
	2228	Squared	26586.2	1.08276	28786.6
	2657	Ranked	216.934	1.00108	216.7
chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60]	1173	Measured	5799.35	1.08735	6305.95
	1311	Squared	24923.6	1.12836	28122.8
	1345	Rooted	62.7228	1.04102	65.296
	1730	Ranked	215.336	1.01303	212.567
choline dehydrogenase. [refseq;acc:nm_018397]	1374	Rooted	62.3839	1.04051	64.9113
	1556	Measured	5875.75	1.07267	6302.76
	1647	Ranked	217.256	1.01451	214.149
	2118	Squared	26865.2	1.08751	29216.1
choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329]	591		23526.5	1.18502	27879.4
	1139	Measured	5790.66	1.08864	6303.95
	1910	Rooted	63.4354	1.02906	65.279
	1967	Ranked	211.632	1.00978	213.702
cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	269		241.373	1.10763	267.352
	323	Rooted	50.3803	1.10923	45.4193
	1840	Measured	3591.95	1.06417	3375.34
	1958	Squared	12175.3	1.09284	13305.6
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]	275	Ranked	241.373	1.10763	267.352
	329	Rooted	50.3803	1.10923	45.4193
	1846	Measured	3591.95	1.06417	3375.34
	1964	Squared	12175.3	1.09284	13305.6
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	151	Rooted	38.8223	1.1977	46.4975
	234	Ranked	287.41	1.11905	256.835
	271	Measured	2554.89	1.21092	3093.78
	1693	Squared	9190.5	1.10551	10160.2
chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]	222	Rooted	52.7936	1.13762	60.0592
	282	Ranked	252.39	1.10553	228.297
	468	Measured	4869.15	1.14558	5578.02
	919	Squared	23346.9	1.15665	27004.3
chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]	800	Rooted	54.1622	1.06481	57.6725

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.