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

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Showing element 301 to 350 of 12912 in total

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

description	Rank	Value Type	green	red	network_comparison
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	1102	Ranked	235.974	229.442	1.02847
	1405	Squared	21974.6	19596.4	1.12136
	2126	Measured	5066.92	4806.33	1.05422
	2682	Rooted	56.8729	56.6826	1.00336
40s ribosomal protein s28. [swissprot;acc:p25112]	352	Squared	38183.6	30682.9	1.24446
	700	Measured	8015.92	7161.14	1.11936
	1171	Rooted	73.7627	70.4215	1.04745
	1982	Ranked	198.427	200.343	1.00966
40s ribosomal protein s29. [swissprot;acc:p30054]	277		267.642	241.849	1.10665
	320	Rooted	45.294	50.2784	1.11005
	1756	Measured	3357.6	3582.57	1.067
	2128	Squared	13163.1	12106.4	1.08728
40s ribosomal protein s3. [swissprot;acc:p23396]	346	Ranked	265.119	241.612	1.09729
	462	Rooted	46.236	50.6274	1.09498
	1980	Squared	14048	12856.2	1.0927
	2235	Measured	3508.13	3674.29	1.04736
40s ribosomal protein s30. [swissprot;acc:q05472]	1002	Rooted	64.6874	61.3513	1.05438
	1081	Ranked	216.875	223.44	1.03027
	1145	Measured	6416.07	5893.97	1.08858
	1195	Squared	31984.1	28134.5	1.13683
40s ribosomal protein s3a. [swissprot;acc:p49241]	867	Ranked	234.674	225.689	1.03981
	1220	Squared	22178	19516.8	1.13635
	2263	Measured	5145.39	4918.64	1.0461
	2623	Rooted	57.434	57.8256	1.00682
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	288	Ranked	266.078	240.758	1.10517
	362	Rooted	45.9477	50.7803	1.10518
	1930	Squared	14029.9	12829.2	1.09359
	1974	Measured	3470.64	3678.62	1.05993
40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	287	Ranked	266.079	240.758	1.10517
	361	Rooted	45.9472	50.7801	1.10518
	1929	Squared	14029.4	12828.8	1.09359
	1967	Measured	3470.55	3678.56	1.05994
40s ribosomal protein s5. [swissprot;acc:p46782]	366	Ranked	265.756	242.473	1.09602
	467	Rooted	46.1093	50.4649	1.09446
	1820	Squared	14290.8	13022.7	1.09738
	2343	Measured	3516.98	3672.17	1.04413
40s ribosomal protein s7 (s8). [swissprot;acc:p23821]	1561	Squared	29098.4	26174.3	1.11172
	1642	Measured	6186.39	5782.92	1.06977
	2102	Rooted	63.5389	61.9958	1.02489
	2149	Ranked	219.366	217.871	1.00686
40s ribosomal protein s8. [swissprot;acc:p09058]	1213	Rooted	64.3044	61.4774	1.04598
	1397	Ranked	214.049	218.64	1.02145
	1471	Measured	6087.55	5659.45	1.07564
	2111	Squared	26984.5	24799.3	1.08812
40s ribosomal protein s9. [swissprot;acc:p46781]	439	Ranked	257.784	238.986	1.07866
	786	Rooted	48.813	52.0101	1.0655
	1746	Squared	15800.8	14357.1	1.10056
	2628	Measured	3877.14	3933.74	1.0146
40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865]	789	Ranked	234.511	224.244	1.04578
	1047	Squared	23353.8	20357.7	1.14717

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.