Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1918 to 1967 of 3228 in total

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

Rank	description	red	green	network_comparison	
1918	seven in absentia homolog 1. [source:refseq;acc:nm_003031]	5394.24	5730.73	1.06238	
1919	hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [source:swissprot;acc:p46597]	5444.6	5783.95	1.06233	
1920	basic proline-rich peptide p-e (ib-9). [source:swissprot;acc:p02811]	6262.66	6652.85	1.0623	
1921	salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [source:swissprot;acc:p10162]	6262.66	6652.85	1.0623	
1922	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [source:swissprot;acc:q16543]	5567.41	5914.05	1.06226	
1923	brain protein 16. [source:refseq;acc:nm_016458]	5774.02	6133.01	1.06217	
1924	transcriptional adaptor 3-like isoform a. [source:refseq;acc:nm_006354]	7260.23	7711.3	1.06213	
1925	bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [source:refseq;acc:nm_013263]	7260.23	7711.29	1.06213	
1926	frg1 protein (fshd region gene 1 protein). [source:swissprot;acc:q14331]	7260.23	7711.3	1.06213	
1927	transcriptional adapter 2-like (ada2-like protein) (kl04p). [source:swissprot;acc:o75478]	7260.23	7711.3	1.06213	
1928	son of sevenless protein homolog 1 (sos-1). [source:swissprot;acc:q07889]	7514.8	7980.22	1.06193	
1929	pxr2b protein. [source:refseq;acc:nm_016559]	6996.51	7429.18	1.06184	
1930	p28 ing5. [source:refseq;acc:nm_032329]	5784.06	6141.48	1.06179	
1931	ring finger protein 25 (ec 6.3.2.-). [source:swissprot;acc:q96bh1]	9946.21	9367.66	1.06176	
1932	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [source:refseq;acc:nm_004712]	10300	9701.33	1.06171	
1933	conserved oligomeric golgi complex component 7. [source:swissprot;acc:p83436]	10300	9701.33	1.06171	
1934	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [source: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). [source:swissprot;acc:o15269]	6167.29	6544.12	1.0611	
1936	williams-beuren syndrome critical region protein 20 copy b. [source: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. [source:refseq;acc:nm_018044]	5171.45	5486.96	1.06101	
1938	williams beuren syndrome chromosome region 20c isoform 1. [source:refseq;acc:nm_032158]	5171.45	5486.96	1.06101	
1939	brca1-associated ring domain protein 1 (bard-1). [source:swissprot;acc:q99728]	5669.9	6015.75	1.061	
1940	m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [source:swissprot;acc:p30307]	4450.17	4721.37	1.06094	
1941	rac gtpase activating protein 1; gtpase activating protein. [source:refseq;acc:nm_013277]	5521.07	5856.93	1.06083	
1942	pre-mrna cleavage factor i, 59 kda subunit. [source:refseq;acc:nm_024811]	5805.06	6158.16	1.06083	
1943	p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [source: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). [source:swissprot;acc:q92830]	7210.64	7648.94	1.06079	
1945	cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [source:swissprot;acc:p23528]	6230.21	6608.64	1.06074	
1946	cofilin, muscle isoform (cofilin 2). [source:swissprot;acc:q9y281]	6230.21	6608.64	1.06074	
1947	transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [source:swissprot;acc:q15542]	7195.76	7632.83	1.06074	
1948	destrin (actin-depolymerizing factor) (adf). [source:swissprot;acc:p18282]	6230.21	6608.64	1.06074	
1949	ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [source:swissprot;acc:q92890]	6230.21	6608.64	1.06074	
1950	glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [source:refseq;acc:nm_018292]	5888.32	6245.89	1.06073	
1951	fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [source:swissprot;acc:o00519]	5888.32	6245.89	1.06073	
1952	coactosin-like protein. [source:swissprot;acc:q14019]	5888.32	6245.89	1.06073	
1953	uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [source:swissprot;acc:p13051]	5888.32	6245.89	1.06073	
1954	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [source:swissprot;acc:o75879]	5888.32	6245.89	1.06073	
1955	28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [source:swissprot;acc:q9y3d3]	5195.3	5510.67	1.0607	
1956	nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [source: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). [source:swissprot;acc:q16514]	7019.78	7444.06	1.06044	
1958	splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [source: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). [source:swissprot;acc:q01081]	5448.35	5777.35	1.06039	
1960	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	5448.35	5777.35	1.06039	
1961	splicing factor u2af 65 kda subunit (u2 auxiliary factor 65 kda subunit) (u2 snrnp auxiliary factor large subunit) (hu2af(65)). [source:swissprot;acc:p26368]	5448.35	5777.35	1.06039	
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). [source:swissprot;acc:q9upt6]	5941.24	6297.78	1.06001	
1963	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [source:swissprot;acc:p00439]	4374.32	4126.96	1.05994	
1964	pp3111 protein. [source:refseq;acc:nm_022156]	4374.32	4126.96	1.05994	
1965	syntaxin 18. [source:swissprot;acc:q9p2w9]	4374.32	4126.96	1.05994	
1966	rd protein. [source:swissprot;acc:p18615]	4374.32	4126.96	1.05994	
1967	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	3678.56	3470.55	1.05994	

Legend:
- Rank is the rank after comparing the two networks
- 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.

- http://analysis.yellowcouch.org/