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

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Showing element 425 to 474 of 8289 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1

Rank	description	Interaction Map	red	green	network_comparison
213	dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512]	Low confidence	209.765	199.755	1.05011
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	High confidence	210.693	186.95	1.127
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]		191.644	170.192	1.12605
	udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294]	Low confidence	206.583	196.743	1.05001
215	a kindred of iglon. [refseq;acc:nm_173808]		199.671	209.654	1.05
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	High confidence	112	126	1.125
216	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]
	neuromedin-b receptor (nmb-r) (neuromedin-b-preferring bombesin receptor). [swissprot;acc:p28336]	Low confidence	199.671	209.654	1.05
217	gastrin-releasing peptide receptor (grp-r) (grp-preferring bombesin receptor). [swissprot;acc:p30550]
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	High confidence	112	126	1.125
218	bombesin receptor subtype-3 (brs-3). [swissprot;acc:p32247]	Low confidence	199.671	209.654	1.05
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	High confidence	112	126	1.125
219	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]
	transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867]	Low confidence	172.647	164.44	1.04991
220	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	High confidence	112	126	1.125
	nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236]	Low confidence	172.647	164.44	1.04991
221	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	High confidence	112	126	1.125
	transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9]	Low confidence	172.647	164.44	1.04991
222	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	High confidence	112	126	1.125
	ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965]	Low confidence	203.935	214.089	1.04979
223	general transcription factor iiic, polypeptide 3, 102kda; general transcription factor iiic, polypeptide 3 (102kd); transcription factor iiic, 102 kd. [refseq;acc:nm_012086]		217.228	206.926
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	High confidence	112	126	1.125
224	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]		185.969	165.623	1.12285
	ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357]	Low confidence	203.933	214.059	1.04965
225	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]		201.41	191.974	1.04915
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	High confidence	226.471	201.769	1.12243
226	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]		239.991	269.238	1.12187
	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]	Low confidence	208.289	198.538	1.04911
227	c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319]		216.404	206.277	1.04909
	thrombospondin 3 precursor. [swissprot;acc:p49746]	High confidence	239.99	269.234	1.12186
228	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]		226.411	202.088	1.12036
	u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012]	Low confidence	202.727	193.31	1.04871
229	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	High confidence	226.401	202.094	1.12028
	toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603]	Low confidence	207.926	198.276	1.04867
230	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	High confidence	239.35	267.915	1.11934
	jm1 protein. [refseq;acc:nm_014008]	Low confidence	216.308	206.292	1.04855
231	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	High confidence	239.336	267.881	1.11927
	mitochondrial import inner membrane translocase subunit tim23. [swissprot;acc:o14925]	Low confidence	220.722	210.645	1.04784
232	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]		214.032	204.284	1.04772
	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	High confidence	239.336	267.879	1.11926
233	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]		239.32	267.842	1.11918
	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	Low confidence	209.649	200.129	1.04757
234	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	High confidence	287.41	256.835	1.11905
	cytochrome p450 51a1 (ec 1.14.13.70) (cypli) (p450li) (sterol 14-alpha demethylase) (lanosterol 14-alpha demethylase) (ldm) (p450-14dm). [swissprot;acc:q16850]	Low confidence	208.851	199.38	1.0475
235	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	High confidence	227.357	254.15	1.11785
	u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579]	Low confidence	202.654	193.53	1.04715
236	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936]		212.056	202.524	1.04707
	pp3111 protein. [refseq;acc:nm_022156]	High confidence	227.357	254.15	1.11785
237	single-minded homolog 1. [swissprot;acc:p81133]	Low confidence	212.056	202.524	1.04707
	syntaxin 18. [swissprot;acc:q9p2w9]	High confidence	227.357	254.15	1.11785

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.