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

Results: HTML CSV LaTeX

Showing element 1868 to 1917 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

Rank	network_comparison	red	description	green
1868	1.0636	6076.66	pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059]	6463.12
1869			integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418]
1870			star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4]	6463.13
1871			ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404]	6463.12
1872			ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283]
1873		3618.46	40s ribosomal protein s11. [swissprot;acc:p04643]	3402.09
1874		6076.66	ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86]	6463.12
1875			keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	6463.14
1876			espin. [refseq;acc:nm_031475]	6463.12
1877			cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635]
1878			pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832]
1879			lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980]
1880			d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917]
1881	1.0635	6076.68	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	6462.56
1882	1.06346	5490.24	eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091]	5838.67
1883	1.06342	5826	26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]	6195.48
1884			adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186]
1885			ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5]
1886			rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763]
1887	1.06335	5438.6	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	5783.11
1888			bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885]
1889		5438.68	testis-specific bromodomain protein. [refseq;acc:nm_001726]	5783.2
1890		5438.6	nag14 protein. [refseq;acc:nm_022143]	5783.11
1891	1.06334	5438.18	bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059]	5782.62
1892		5438.52	bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440]	5783.01
1893	1.06319	6830.4	acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510]	7261.98
1894	1.06308	3598.08	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	3384.59
1895	1.063	5882.1	ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265]	6252.66
1896	1.06285	4521	m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304]	4805.16
1897	1.06282	4590.74	thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541]	4879.11
1898	1.0628	6885.11	3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	7317.48
1899	1.06269	5786.36	ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [swissprot;acc:q9y230]	6149.1
1900	1.06266	5399.47	seven in absentia homolog 2. [refseq;acc:nm_005067]	5737.79
1901	1.06261	5204.25	inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181]	5530.11
1902			inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869]
1903			aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9]
1904			ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170]
1905	1.06257	7497.96	son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890]	7967.09
1906	1.06251	5396.61	mitochondrial ribosomal protein l18. [refseq;acc:nm_014161]	5733.93
1907	1.06246	6858.84	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	7287.27
1908			dc11 protein. [refseq;acc:nm_020186]
1909			amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905]
1910			5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557]
1911			ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968]
1912			ubiquitin-activating enzyme e1 (a1s9 protein). [swissprot;acc:p22314]
1913			calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746]
1914			melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194]
1915			5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]
1916			calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0]
1917			acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561]

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.