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

Results: HTML CSV LaTeX

Showing element 1880 to 1929 of 12912 in total

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

Rank	Hugo	description	red	green	network_comparison
1880	DRD4	d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917]	6076.66	6463.12	1.0636
1881	no value	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	6076.68	6462.56	1.0635
1882	EIF2S3	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	PSMD1	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	ADRM1	adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186]
1885	UCHL5	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	C19orf2	rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763]
1887	no value	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	5438.6	5783.11	1.06335
1888	BRD4	bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885]
1889	BRDT	testis-specific bromodomain protein. [refseq;acc:nm_001726]	5438.68	5783.2
1890	LRRC4	nag14 protein. [refseq;acc:nm_022143]	5438.6	5783.11
1891	BRD3	bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059]	5438.18	5782.62	1.06334
1892	BRD2	bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440]	5438.52	5783.01
1893	ASAH1	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	no value	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	3598.08	3384.59	1.06308
1895	RUVBL1	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	CDC25A	m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304]	4521	4805.16	1.06285
1897	GLRX3	thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541]	4590.74	4879.11	1.06282
1898	no value	3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	6885.11	7317.48	1.0628
1899	RUVBL2	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	SIAH2	seven in absentia homolog 2. [refseq;acc:nm_005067]	5399.47	5737.79	1.06266
1901	PPA1	inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181]	5204.25	5530.11	1.06261
1902	PPA2	inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869]
1903	AIPL1	aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9]
1904	AIP	ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170]
1905	SOS2	son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890]	7497.96	7967.09	1.06257
1906	MRPL18	mitochondrial ribosomal protein l18. [refseq;acc:nm_014161]	5396.61	5733.93	1.06251
1907	no value	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	APPBP1	amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905]
1910	ALAS2	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	UBE1C	ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968]
1912	UBE1	ubiquitin-activating enzyme e1 (a1s9 protein). [swissprot;acc:p22314]
1913	SLC25A12	calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746]
1914	HHAT	melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194]
1915	ALAS1	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]
1916	SLC25A13	calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0]
1917	NDUFAB1	acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561]
1918	no value	seven in absentia homolog 1. [refseq;acc:nm_003031]	5394.24	5730.73	1.06238
1919		hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597]	5444.6	5783.95	1.06233
1920		basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	6262.66	6652.85	1.0623
1921	PRB4	salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [swissprot;acc:p10162]
1922	CDC37	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	5567.41	5914.05	1.06226
1923	no value	brain protein 16. [refseq;acc:nm_016458]	5774.02	6133.01	1.06217
1924	TADA3L	transcriptional adaptor 3-like isoform a. [refseq;acc:nm_006354]	7260.23	7711.3	1.06213
1925	BRD7	bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263]		7711.29
1926	FRG1	frg1 protein (fshd region gene 1 protein). [swissprot;acc:q14331]		7711.3
1927	TADA2L	transcriptional adapter 2-like (ada2-like protein) (kl04p). [swissprot;acc:o75478]
1928	SOS1	son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889]	7514.8	7980.22	1.06193
1929	PEX5L	pxr2b protein. [refseq;acc:nm_016559]	6996.51	7429.18	1.06184

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
- Hugo is the HGNC identifier if it exists
- 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.