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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 19268 in total

red  : 0
Network Comparison Type  : Subtracted
Value Type  : Measured

Rank	description	Filtered	green	Interaction Map	network_comparison
185	cab2. [refseq;acc:nm_033419]	0	174	High confidence	174
265	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]		109		109
289	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		89		89
290	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
291	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
342	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]		59		59
376	sedlin. [swissprot;acc:o14582]		43		43
377	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
428	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]		18		18
461	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		89	Low confidence	89
462	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
463	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
494	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]		0	High confidence	0
495	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
496	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
497	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
498	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
499	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
500	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
501	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
502	brca1 associated protein. [refseq;acc:nm_006768]
554	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]		59	Low confidence	59
755	jumonji protein. [swissprot;acc:q92833]		17.5166		17.5166
837	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]		0		0
838	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
839	cobw-like protein. [refseq;acc:nm_018491]
840	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
841	gamma-glutamyltransferase. [sptrembl;acc:q14390]
842	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
843	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
2756	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	1		High confidence
2757	nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209]
2758	nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [swissprot;acc:q9ulw6]
2759	retinoic acid receptor rxr-alpha. [swissprot;acc:p19793]
2760	t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [swissprot;acc:q16559]
2761	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]
2762	developmentally regulated gtp-binding protein 1 (drg 1). [swissprot;acc:q9y295]
2763	ring finger protein 3. [refseq;acc:nm_006315]
2764	ras-related protein rab-11b (gtp-binding protein ypt3). [swissprot;acc:q15907]
2765	histone h2a.e (h2a/e). [swissprot;acc:q99878]
2766	ss18-like protein 1 (syt homolog-1). [swissprot;acc:o75177]
2767	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
2768	histone h2a.x (h2a/x). [swissprot;acc:p16104]
2769	histone h2a.q (h2a/q) (h2a-gl101) (fragment). [swissprot;acc:q16777]
2770	nipsnap1 protein. [swissprot;acc:q9bpw8]
2771	t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435]
2772	uridine diphosphate glucose pyrophosphatase. [refseq;acc:nm_177533]
2773	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]
2774	dc12 protein. [refseq;acc:nm_020187]
2775	jerky protein homolog like (hhmjg). [swissprot;acc:q9y4a0]

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.