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

Results: HTML CSV LaTeX

Showing element 1651 to 1700 of 29840 in total

Interaction Map	High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison	
104	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Squared	Divided	1	407289	263351	1.54656	
104	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4v7]	Rooted	Divided	0	13.7413	17.8164	1.29656	
104	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [source:refseq;acc:nm_004839]	Ranked	Divided	1	252.371	202.016	1.24926	
104	jun dimerization protein. [source:refseq;acc:nm_130469]	Rooted	Divided	1	60.8365	77.7233	1.27758	
104	likely ortholog of mouse variant polyadenylation protein cstf-64. [source:refseq;acc:nm_015235]	Squared	Subtracted	1	121579	87259.3	34319.7	
104	metabotropic glutamate receptor 3 precursor (mglur3). [source:swissprot;acc:q14832]	Squared	Divided	0	0.70501	1.50296	2.13183	
104	musashi 2 isoform a. [source:refseq;acc:nm_138962]	Measured	Divided	1	4241.57	5810.79	1.36996	
104	nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	Measured	Divided	0	5106.93	7500.75	1.46874	
104	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [source:swissprot;acc:q15765]	Ranked	Divided	0	9545	7868	1.21314	
104	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	Rooted	Subtracted	1	19.9625	35.798	15.8355	
104	sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [source:swissprot;acc:q9nzq3]	Ranked	Subtracted	0	18809.5	16764.2	2045.3	
104	soluble liver antigen/liver pancreas antigen. [source:refseq;acc:nm_153825]	Measured	Subtracted	0	688.436	385.626	302.81	
104	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	Ranked	Subtracted	1	256.228	298.438	42.21	
104	tigger transposable element derived 6. [source:refseq;acc:nm_030953]	Rooted	Subtracted	0	13.0605	17.6725	4.612	
105	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [source:swissprot;acc:p45954]	Ranked	Divided	0	17410.5	14360	1.21243	
105	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [source:swissprot;acc:p35606]	Measured	Subtracted	0	5427.25	5130.58	296.67	
105	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Squared	Divided	1	407289	263351	1.54656	
105	dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	Squared	Divided	0	2.36686	4.90793	2.0736	
105	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [source:sptrembl;acc:q9uge0]	Squared	Subtracted	0	600.627	1860.93	1260.3	
105	fos-related antigen 2. [source:swissprot;acc:p15408]	Measured	Divided	0	3233.86	2208.1	1.46454	
105	fos-related antigen 2. [source:swissprot;acc:p15408]	Rooted	Divided	1	60.8675	77.7168	1.27682	
105	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [source:swissprot;acc:p49448]	Rooted	Divided	0	25.8353	33.3747	1.29183	
105	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [source:swissprot;acc:p04901]	Ranked	Divided	1	266.716	333.165	1.24914	
105	musashi 1. [source:refseq;acc:nm_002442]	Measured	Divided	1	4241.57	5810.79	1.36996	
105	neuroendocrine differentiation factor; comparative gene identification transcript 149. [source:refseq;acc:nm_016079]	Measured	Subtracted	1	11068	8508.5	2559.5	
105	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967]	Squared	Subtracted	1	90432.9	56304.2	34128.7	
105	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [source:swissprot;acc:q00007]	Rooted	Subtracted	1	63.7477	48.1588	15.5889	
105	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [source:swissprot;acc:p50993]	Ranked	Subtracted	0	11853.5	9808.86	2044.64	
105	tigger transposable element derived 7; jerky (mouse) homolog-like. [source:refseq;acc:nm_033208]	Rooted	Subtracted	0	13.0525	17.6565	4.604	
105	transcription factor jun-d. [source:swissprot;acc:p17535]	Ranked	Subtracted	1	200.941	158.941	42	
106	brain protein 16. [source:refseq;acc:nm_016458]	Ranked	Subtracted	0	6890.54	4854.99	2035.55	
106	casein kinase i alpha s-like. [source:refseq;acc:nm_145203]	Squared	Subtracted	0	7795.92	9052.52	1256.6	
106	cytohesin 4. [source:swissprot;acc:q9uia0]	Squared	Divided	1	407289	263351	1.54656	
106	elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [source:swissprot;acc:p43897]	Ranked	Divided	0	16290.7	13464.8	1.20987	
106	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [source:swissprot;acc:p12268]	Measured	Subtracted	0	712.071	416.524	295.547	
106	nostrin. [source:refseq;acc:nm_052946]	Ranked	Subtracted	1	209.299	249.187	39.888	
106	nuclear protein ukp68. [source:refseq;acc:nm_024824]	Measured	Divided	1	4241.57	5810.79	1.36996	
106	protein fosb (g0/g1 switch regulatory protein 3). [source:swissprot;acc:p53539]	Rooted	Divided	1	60.8692	77.7165	1.27678	
106	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	Measured	Subtracted	1	11068	8508.5	2559.5	
106	rna polymerase i transcription factor rrn3. [source:refseq;acc:nm_018427]	Squared	Divided	0	299.137	144.414	2.07139	
106	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [source:swissprot;acc:o43236]	Squared	Subtracted	1	82624.3	115061	32436.7	
106	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [source:swissprot;acc:q13888]	Measured	Divided	0	1251.66	858.525	1.45792	
106	tigger transposable element derived 1; jerky (mouse) homolog-like. [source:refseq;acc:nm_145702]	Rooted	Subtracted	0	13.0522	17.6559	4.6037	
106	transcription initiation factor iie, beta subunit (tfiie-beta). [source:swissprot;acc:p29084]	Rooted	Divided	0	5.47723	7.07107	1.29099	
106	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [source:swissprot;acc:q99807]	Ranked	Divided	1	252.329	202.004	1.24913	
106	uncharacterized hematopoietic stem/progenitor cells protein mds026. [source:sptrembl;acc:q9nz48]	Rooted	Subtracted	1	63.7477	48.1589	15.5888	
107	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	Measured	Divided	1	4266.04	5843.51	1.36977	
107	60s ribosomal protein l7. [source:swissprot;acc:p18124]	Measured	Subtracted	0	1915.27	2206.07	290.8	
107	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [source:swissprot;acc:p12532]	Ranked	Subtracted	0	9183.49	11217.7	2034.21	
107	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Squared	Divided	1	407289	263351	1.54656	

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/