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

Results: HTML CSV LaTeX

Showing element 25 to 74 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Ranked	1	15	28	1.86667
	hbs1-like. [refseq;acc:nm_006620]	Measured		2597.5	698.5	3.71868
		Squared		1596.92	115.48	13.8285
		Rooted		50.9657	26.4292	1.92839
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured	0	0.00001	89	8900000
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Ranked		8906	21883	2.45711
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Squared		0.00001	2.81207	281207
		Rooted			10.4403	1044030
5	cytohesin 4. [swissprot;acc:q9uia0]	Ranked	1	15	28	1.86667
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared	0	0.00001	1.87479	187479
		Rooted			9.43398	943398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Measured			89	8900000
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]		1	1153.5	339.5	3.39764
		Squared		314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Ranked	0	5510.5	11965.7	2.17144
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		1	15	28	1.86667
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Measured	0	0.00001	89	8900000
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Squared			1.87479	187479
		Rooted			9.43398	943398
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Measured	1	1153.5	339.5	3.39764
		Squared		314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
	ubiquitin protein ligase. [refseq;acc:nm_130466]	Ranked	0	7523	15339.2	2.03897
7	cab2. [refseq;acc:nm_033419]			21866	10950	1.99689
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		1	215	322	1.49767
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Squared	0	0.00001	1.87479	187479
		Rooted			9.43398	943398
	sedlin. [swissprot;acc:o14582]	Measured			43	4300000
	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	1153.5	339.5	3.39764
		Squared		314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
8	db83 protein. [swissprot;acc:p57088]	Measured		1153.5	339.5	3.39764
		Squared		314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
	ero1-like. [refseq;acc:nm_014584]	Squared	0	1.59148	0.00001	159148
		Rooted		9.05539		905539
	hbs1-like. [refseq;acc:nm_006620]	Ranked	1	215	322	1.49767
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		0	11525	21888	1.89918
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Measured		0.00001	43	4300000
9	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]			85	6410	75.4118
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	Squared		0.852071	0.00001	85207.1
		Rooted		7.74597		774597
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Measured	1	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Ranked	0	11525	21888	1.89918
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]		1	212	309	1.45755
10	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	14178.1	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]	Squared		0.00001	0.823905	82390.5

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.