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	Network Comparison Type	Filtered	Interaction Map	red	network_comparison	green

Results: HTML CSV LaTeX

Showing element 5908 to 5957 of 7460 in total

Value Type  : Measured
Interaction Map  : High confidence

description	Rank	Network Comparison Type	Filtered	red	network_comparison	green
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	2143	Divided	1	5859.1	1.05369	6173.7
sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368]	2075	Subtracted			314.6
	2141	Divided			1.05369
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]	43	Subtracted	0	4089.65	606.71	4696.36
	228	Divided			1.14835
	484	Subtracted	1	7139.5	854.56	7994.06
	683	Divided			1.11969
sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962]	488	Subtracted		7105.27	848.44	7953.71
	697	Divided			1.11941
sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963]	491	Subtracted		7067.46	841.81	7909.27
	702	Divided			1.11911
shc transforming protein. [swissprot;acc:p29353]	1821			5633.44	1.06454	5997
	1889	Subtracted			363.56
short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547]	2700	Divided		5239.33	1.00395	5260
	2701	Subtracted			20.67
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	647	Divided		5167.88	1.12481	4594.43
	896	Subtracted			573.45
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	652	Divided		5168.43	1.1242	4597.44
	906	Subtracted			570.99
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	594			6089.21	746.13	6835.34
	659	Divided			1.12253
shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5]	2556			4883.73	1.0203	4982.88
	2567	Subtracted			99.15
signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624]	2206			5833.01	273.47	6106.48
	2248	Divided			1.04688
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9]	757			5622.89	1.11331	6260.02
	771	Subtracted			637.13
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	217	Divided	0	903.967	1.17199	771.309
	240	Subtracted			132.658
	260	Divided	1	4244.95	1.22343	5193.42
	261			4247.36	1.22255	5192.61
	379	Subtracted		4244.95	948.47	5193.42
	383			4247.36	945.25	5192.61
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	393		0	3855.78	30.05	3825.73
	471	Divided			1.00785
	896		1	5208.27	1.10155	5737.17
	1051	Subtracted			528.9
signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224]	2306			5514.81	240.29	5755.1
	2359	Divided			1.04357
signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763]	2304	Subtracted		5514.85	240.32	5755.17
	2357	Divided			1.04358
signal transducer and activator of transcription 4. [swissprot;acc:q14765]	2305	Subtracted		5514.83	240.31	5755.14
	2358	Divided			1.04358
signal transducer and activator of transcription 5a. [swissprot;acc:p42229]	2300	Subtracted		5516.67	241.55	5758.22
	2354	Divided			1.04379
signal transducer and activator of transcription 5b. [swissprot;acc:p51692]	2299	Subtracted		5516.82	241.66	5758.48
	2353	Divided			1.0438
signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226]	2303	Subtracted		5515.12	240.51	5755.63
	2356	Divided			1.04361
signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473]	321	Subtracted		11797.1	1046.9	10750.2

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.