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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 75 to 124 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
10	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]	Rooted	0	0.00001	7.68115	768115
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Measured		85	6410	75.4118
	protein x 0004. [refseq;acc:nm_016301]	Ranked	1	212	309	1.45755
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Measured		398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Measured		398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Ranked	0	11627	6248	1.86092
	rad50-interacting protein 1. [refseq;acc:nm_021930]		1	337	232	1.45259
	sedlin. [swissprot;acc:o14582]	Squared	0	0.00001	0.437633	43763.3
		Rooted			6.55744	655744
	serpin b12. [swissprot;acc:q96p63]	Measured		199.549	5.56738	35.8425
12	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]		1	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	Ranked	0	9429.18	5208.84	1.81023
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Measured		199.249	5.71669	34.8539
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Ranked	1	337	232	1.45259
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Squared	0	0.00001	0.437633	43763.3
		Rooted			6.55744	655744
13	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Measured		1363	47	29
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]		1	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
	dok-like protein. [refseq;acc:nm_024872]	Squared	0	0.289941	0.00001	28994.1
		Rooted		5.91608		591608
	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	Ranked		5210.5	9264.5	1.77804
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]		1	288.754	212.554	1.3585
14	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Squared	0	1.73869	19295.9	11098
	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Measured		130.512	6.50325	20.0687
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Ranked	1	56.6768	75.3531	1.32952
	dystrophin. [swissprot;acc:p11532]		0	10232.5	18054.8	1.76446
	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]	Rooted		0.00001	4.24264	424264
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Measured	1	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
15	gbp protein isoform a. [refseq;acc:nm_017870]			23.9771	42.4773	1.77158
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Squared	0	1.73869	19295.9	11098
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Ranked	1	56.7244	75.3948	1.32914
	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	Rooted	0	4.24264	0.00001	424264
	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	Measured		10	156	15.6
		Ranked		19403	11267	1.72211
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Measured	1	2671	871	3.06659
		Squared		1688.58	179.56	9.40399
16	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Ranked	0	12170.7	20670.6	1.69839
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]		1	56.7252	75.3954	1.32913
	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]	Squared	0	0.00001	0.0766864	7668.64
	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	Measured		1	15	15

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.