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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	Value Type	description	Filtered	red	network_comparison	green
7	Ranked	cab2. [refseq;acc:nm_033419]	0	21866	1.99689	10950
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	215	1.49767	322
	Squared	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	0.00001	187479	1.87479
		sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	1	314.926	11.544	27.2805
	Rooted	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	0.00001	943398	9.43398
		sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	1	33.9632	1.84327	18.4255
8	Measured	db83 protein. [swissprot;acc:p57088]		1153.5	3.39764	339.5
		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0	0.00001	4300000	43
	Ranked	hbs1-like. [refseq;acc:nm_006620]	1	215	1.49767	322
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0	11525	1.89918	21888
	Squared	db83 protein. [swissprot;acc:p57088]	1	314.926	11.544	27.2805
		ero1-like. [refseq;acc:nm_014584]	0	1.59148	159148	0.00001
	Rooted	db83 protein. [swissprot;acc:p57088]	1	33.9632	1.84327	18.4255
		ero1-like. [refseq;acc:nm_014584]	0	9.05539	905539	0.00001
9	Measured	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		85	75.4118	6410
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	1	398.5	3.21581	1281.5
	Ranked	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0	11525	1.89918	21888
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	1	212	1.45755	309
	Squared	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	0	0.852071	85207.1	0.00001
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	1	37.5863	10.3414	388.696
	Rooted	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	0	7.74597	774597	0.00001
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	1	19.9625	1.79326	35.798
10	Measured	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	0	85	75.4118	6410
		tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	1	398.5	3.21581	1281.5
	Ranked	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	0	7509.39	1.88805	14178.1
		protein x 0004. [refseq;acc:nm_016301]	1	212	1.45755	309
	Squared	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	0.00001	82390.5	0.823905
		tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	1	37.5863	10.3414	388.696
	Rooted	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	0.00001	768115	7.68115
		tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	1	19.9625	1.79326	35.798
11	Measured	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]		398.5	3.21581	1281.5
		serpin b12. [swissprot;acc:q96p63]	0	199.549	35.8425	5.56738
	Ranked	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]		11627	1.86092	6248
		rad50-interacting protein 1. [refseq;acc:nm_021930]	1	337	1.45259	232
	Squared	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]		37.5863	10.3414	388.696
		sedlin. [swissprot;acc:o14582]	0	0.00001	43763.3	0.437633
	Rooted	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	1	19.9625	1.79326	35.798
		sedlin. [swissprot;acc:o14582]	0	0.00001	655744	6.55744
12	Measured	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	1	398.5	3.21581	1281.5
		hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	0	199.249	34.8539	5.71669
	Ranked	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]		9429.18	1.81023	5208.84
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	337	1.45259	232
	Squared	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]		37.5863	10.3414	388.696
		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0	0.00001	43763.3	0.437633
	Rooted	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	1	19.9625	1.79326	35.798
		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	0	0.00001	655744	6.55744
13	Measured	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		1363	29	47
		cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	1	398.5	3.21581	1281.5
	Ranked	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	0	5210.5	1.77804	9264.5
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	1	288.754	1.3585	212.554

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.