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 1930 to 1979 of 3228 in total

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

Rank	description	red	green	network_comparison
1930	p28 ing5. [refseq;acc:nm_032329]	5784.06	6141.48	1.06179
1931	ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1]	9946.21	9367.66	1.06176
1932	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	10300	9701.33	1.06171
1933	conserved oligomeric golgi complex component 7. [swissprot;acc:p83436]
1934	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]	5949.31	6313.1	1.06115
1935	serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269]	6167.29	6544.12	1.0611
1936	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	5171.45	5486.96	1.06101
1937	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]
1938	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]
1939	brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728]	5669.9	6015.75	1.061
1940	m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307]	4450.17	4721.37	1.06094
1941	rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277]	5521.07	5856.93	1.06083
1942	pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811]	5805.06	6158.16
1943	p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831]	7210.87	7649.23	1.06079
1944	general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [swissprot;acc:q92830]	7210.64	7648.94
1945	cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528]	6230.21	6608.64	1.06074
1946	cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281]
1947	transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [swissprot;acc:q15542]	7195.76	7632.83
1948	destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282]	6230.21	6608.64
1949	ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890]
1950	glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292]	5888.32	6245.89	1.06073
1951	fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519]
1952	coactosin-like protein. [swissprot;acc:q14019]
1953	uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051]
1954	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]
1955	28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3]	5195.3	5510.67	1.0607
1956	nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062]	4689.78	4973.44	1.06048
1957	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514]	7019.78	7444.06	1.06044
1958	splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [refseq;acc:nm_016333]	5448.35	5777.35	1.06039
1959	splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [swissprot;acc:q01081]
1960	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]
1961	splicing factor u2af 65 kda subunit (u2 auxiliary factor 65 kda subunit) (u2 snrnp auxiliary factor large subunit) (hu2af(65)). [swissprot;acc:p26368]
1962	c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [swissprot;acc:q9upt6]	5941.24	6297.78	1.06001
1963	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	4374.32	4126.96	1.05994
1964	pp3111 protein. [refseq;acc:nm_022156]
1965	syntaxin 18. [swissprot;acc:q9p2w9]
1966	rd protein. [swissprot;acc:p18615]
1967	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	3678.56	3470.55
1968	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	4374.32	4126.96
1969	androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]
1970	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]
1971	j domain containing protein 1. [swissprot;acc:q9ukb3]
1972	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]
1973	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]
1974	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	3678.62	3470.64	1.05993
1975	cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129]	6988.29	7406.53	1.05985
1976	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519]	5939.85	6294.91	1.05978
1977	lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [refseq;acc:nm_005358]	5782.86	6126.69	1.05946
1978	uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725]	5475.74	5800.97	1.05939
1979	26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036]

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.