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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 32 of 32 in total

Rank  : 46

green	description	Filtered	network_comparison	Value Type	Interaction Map	red	Network Comparison Type
5.80679	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	0	1.69589	Rooted	Low confidence	9.84765	Divided
7.48331	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]		1.67439		High confidence	12.53
9.07489	fos39347_1. [sptrembl;acc:o75863]		5.67971		Low confidence	14.7546	Subtracted
33.2721	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]		8.102		High confidence	25.1701
43.9629	deltex 2. [refseq;acc:nm_020892]	1	1.5909			27.634	Divided
67	ephrin type-b receptor 4 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor htk). [swissprot;acc:p54760]	0	2.79167	Measured	Low confidence	24
67.6572	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	1	7.9751	Rooted		75.6323	Subtracted
75.4064	jun dimerization protein. [refseq;acc:nm_130469]		1.13252			66.5831	Divided
83.274	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	0	5.60534	Squared	High confidence	14.8562
98.4675	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]		5.87971		Low confidence	16.747
120.823	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	1	16.623	Rooted	High confidence	137.446	Subtracted
161.068	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]		1.27053	Ranked		204.642	Divided
217.217	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]		25.525		Low confidence	242.742	Subtracted
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]		1.11751				Divided
266.948	neuralized-like. [refseq;acc:nm_004210]		65.378		High confidence	332.326	Subtracted
438.035	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	0	2.16674	Measured		202.163	Divided
1390.33	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	1	1.78438			779.167
2436.4	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	0	587.45			3023.85	Subtracted
4196.79	putative dynein light chain protein dj8b22.1. [swissprot;acc:q9y3p0]		411.04		Low confidence	4607.83
9264.5	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]		4054	Ranked	High confidence	5210.5
9645.34	transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867]	1	1.16027	Measured	Low confidence	8313.02	Divided
12942.3	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]		1326.3			11616	Subtracted
13210.4	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0	1.31424	Ranked		17361.7	Divided
17020.5	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]		3195			13825.5	Subtracted
18499.2	60s ribosomal protein l37a. [swissprot;acc:p12751]		1.42943		High confidence	12941.7	Divided
20431.7	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	1	4464.7	Measured		24896.4	Subtracted
24837.5	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	0	5357.5	Squared		30195
35675.5	beta-tubulin 4q. [sptrembl;acc:q8wz78]		5005.7		Low confidence	40681.2
61881.5	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	1	20466.3			82347.8
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]		1.33073				Divided
73157.5	apg3p; pc3-96 protein. [refseq;acc:nm_022488]		1.77148		High confidence	129597
136779	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]		73666			210445	Subtracted

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.