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 6408 to 6457 of 7460 in total

Value Type  : Measured
Interaction Map  : High confidence

description	Rank	Network Comparison Type	Filtered	red	network_comparison	green
t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435]	2771	Subtracted	1	0	0	0
t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]	1539			6179.59	433.56	6613.15
	1632	Divided			1.07016
t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]	2697			5176.92	1.00436	5154.43
	2699	Subtracted			22.49
t-cell activation wd repeat protein. [refseq;acc:nm_139281]	831	Divided		4062.03	1.10597	4492.48
	1557	Subtracted			430.45
t-cell acute lymphocytic leukemia-1 protein (tal-1 protein) (stem cell protein) (t-cell leukemia/lymphoma-5 protein). [swissprot;acc:p17542]	2865	Divided		0.00001	1	0.00001
		Subtracted		0	0	0
t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [swissprot;acc:q16559]	2760	Divided		0.00001	1	0.00001
		Subtracted		0	0	0
t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314]	2568	Divided		3964.71	1.01968	4042.75
	2621	Subtracted			78.04
t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763]	2567	Divided			1.01968
	2620	Subtracted			78.04
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711]	2564	Divided			1.01968
	2617	Subtracted			78.04
t-complex 11. [refseq;acc:nm_018679]	2266			6327.14	252.24	6579.38
	2392	Divided			1.03987
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808]	606	Subtracted		10231.8	744.46	9487.34
	1370	Divided			1.07847
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	128	Subtracted		11004.2	1940	12944.2
	356	Divided			1.1763
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	201			4810.22	1.26294	6075.04
	270	Subtracted			1264.82
t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643]	691			8425.35	673.78	7751.57
	1194	Divided			1.08692
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	111	Subtracted		12365.2	2459.7	14824.9
	307	Divided			1.19892
t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227]	196		0	465.37	1.20782	562.085
	276	Subtracted			96.715
	2917	Divided	1	0.00001	1	0.00001
		Subtracted		0	0	0
t-complex protein 1, zeta-2 subunit (tcp-1-zeta-2) (cct-zeta-2) (tcp- 1-zeta-like) (cct-zeta-like) (testis-specific tcp20) (testis-specific protein tsa303). [swissprot;acc:q92526]	2995	Divided		0.00001	1	0.00001
		Subtracted		0	0	0
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	56	Divided		1631.67	1.63302	2664.55
	335	Subtracted			1032.88
t54 protein. [swissprot;acc:q92917]	2186			6362.48	284.94	6647.42
	2320	Divided			1.04478
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	391			3658.76	1.16358	3144.39
	1118	Subtracted			514.37
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	654			6455.66	713.16	7168.82
	802	Divided			1.11047
target of myb protein 1. [swissprot;acc:o60784]	792	Subtracted		5640.79	615.06	6255.85
	812	Divided			1.10904
target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678]	795	Subtracted		5641.53	614.64	6256.17
	816	Divided			1.10895
tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226]	894	Subtracted		6599.84	574.45	7174.29
	1192	Divided			1.08704
tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885]	2371	Subtracted		8542.13	198.1	8740.23

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.