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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 14920 in total

Filtered  : 0
Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	green	Value Type	red	network_comparison
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	Ranked	4294	3.70633
	cab2. [refseq;acc:nm_033419]	7.16592	Squared	0.00001	716592
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	Measured	364	36400000
			Rooted	19.0788	1907880
2	cab2. [refseq;acc:nm_033419]	174	Measured	0.00001	17400000
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	Ranked	5865	2.55362
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	Squared	5.61325	561325
			Rooted	12.4097	1240970
3	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	11083.9	Ranked	4475.84	2.47638
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109	Measured	0.00001	10900000
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001	Squared	5.61325	561325
			Rooted	12.4097	1240970
4	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	Measured	0.00001	8900000
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	Ranked	8906	2.45711
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	2.81207	Squared	0.00001	281207
		10.4403	Rooted		1044030
5	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	1.87479	Squared		187479
		9.43398	Rooted		943398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	89	Measured		8900000
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	11965.7	Ranked	5510.5	2.17144
6	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	89	Measured	0.00001	8900000
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	1.87479	Squared		187479
		9.43398	Rooted		943398
	ubiquitin protein ligase. [refseq;acc:nm_130466]	15339.2	Ranked	7523	2.03897
7	cab2. [refseq;acc:nm_033419]	10950		21866	1.99689
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	1.87479	Squared	0.00001	187479
		9.43398	Rooted		943398
	sedlin. [swissprot;acc:o14582]	43	Measured		4300000
8	ero1-like. [refseq;acc:nm_014584]	0.00001	Squared	1.59148	159148
			Rooted	9.05539	905539
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	21888	Ranked	11525	1.89918
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	43	Measured	0.00001	4300000
9	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410		85	75.4118
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	0.00001	Squared	0.852071	85207.1
			Rooted	7.74597	774597
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	21888	Ranked	11525	1.89918
10	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	14178.1		7509.39	1.88805
	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	0.823905	Squared	0.00001	82390.5
		7.68115	Rooted		768115
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	6410	Measured	85	75.4118
11	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	6248	Ranked	11627	1.86092
	sedlin. [swissprot;acc:o14582]	0.437633	Squared	0.00001	43763.3
		6.55744	Rooted		655744
	serpin b12. [swissprot;acc:q96p63]	5.56738	Measured	199.549	35.8425
12	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	5208.84	Ranked	9429.18	1.81023
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	5.71669	Measured	199.249	34.8539
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0.437633	Squared	0.00001	43763.3
		6.55744	Rooted		655744
13	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	47	Measured	1363	29
	dok-like protein. [refseq;acc:nm_024872]	0.00001	Squared	0.289941	28994.1

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.