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 1863 to 1912 of 3228 in total

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

Rank	description	red	green	network_comparison
1863	keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690]	6076.66	6463.14	1.0636
1864	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]
1865	star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2]		6463.12
1866	keratin associated protein 4.4. [refseq;acc:nm_032524]		6463.14
1867	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]		6463.12
1868	pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059]
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	40s ribosomal protein s11. [swissprot;acc:p04643]	3618.46	3402.09
1874	ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86]	6076.66	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	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	6076.68	6462.56	1.0635
1882	eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091]	5490.24	5838.67	1.06346
1883	26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]	5826	6195.48	1.06342
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	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	5438.6	5783.11	1.06335
1888	bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885]
1889	testis-specific bromodomain protein. [refseq;acc:nm_001726]	5438.68	5783.2
1890	nag14 protein. [refseq;acc:nm_022143]	5438.6	5783.11
1891	bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059]	5438.18	5782.62	1.06334
1892	bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440]	5438.52	5783.01
1893	acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510]	6830.4	7261.98	1.06319
1894	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	3598.08	3384.59	1.06308
1895	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]	5882.1	6252.66	1.063
1896	m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304]	4521	4805.16	1.06285
1897	thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541]	4590.74	4879.11	1.06282
1898	3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	6885.11	7317.48	1.0628
1899	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]	5786.36	6149.1	1.06269
1900	seven in absentia homolog 2. [refseq;acc:nm_005067]	5399.47	5737.79	1.06266
1901	inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181]	5204.25	5530.11	1.06261
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	son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890]	7497.96	7967.09	1.06257
1906	mitochondrial ribosomal protein l18. [refseq;acc:nm_014161]	5396.61	5733.93	1.06251
1907	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	6858.84	7287.27	1.06246
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]

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.