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 Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 630 to 679 of 3730 in total

Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	red	green	network_comparison	
315	ribosome biogenesis regulatory protein homolog. [source:swissprot;acc:q15050]	1	21370.8	17896.5	1.19413	
316	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [source:swissprot;acc:p16870]	0	525	576	1.09714	
316	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [source:swissprot;acc:p08129]	1	21370.8	17896.5	1.19413	
317	adiponectin receptor 2. [source:refseq;acc:nm_024551]	1	3153.1	3762.56	1.19329	
317	my016 protein. [source:sptrembl;acc:q9h3k6]	0	1770.21	1615.47	1.09579	
318	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	1	34190.9	40795.8	1.19318	
318	protein cgi-147. [source:swissprot;acc:q9y3e5]	0	8396.12	9192.38	1.09484	
319	cell division protein kinase 3 (ec 2.7.1.-). [source:swissprot;acc:q00526]	0	1388.45	1268.19	1.09483	
319	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	1	20911	24908.5	1.19117	
320	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	1	20911	24908.5	1.19117	
320	syntaxin 1a (neuron-specific antigen hpc-1). [source:swissprot;acc:q16623]	0	142.802	156.3	1.09452	
321	dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [source:swissprot;acc:p31513]	0	628.072	686.693	1.09333	
321	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	1	20911	24908.5	1.19117	
322	60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	0	1621.1	1771.04	1.09249	
322	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [source:refseq;acc:nm_018685]	1	20911	24908.5	1.19117	
323	histone deacetylase 2 (hd2). [source:swissprot;acc:q92769]	0	2056.14	2244.06	1.09139	
323	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	1	4620.76	5501.94	1.1907	
324	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	1	28136.5	33457.6	1.18912	
324	testis-specific chromodomain y protein 1. [source:swissprot;acc:q9y6f8]	0	3036.29	2784.08	1.09059	
325	septin-like protein kiaa0202 (fragment). [source:swissprot;acc:q92599]	1	16177.9	19235.4	1.18899	
325	testis-specific chromodomain protein y protein 2. [source:swissprot;acc:q9y6f7]	0	3036.85	2784.59	1.09059	
326	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	1	3432.96	4081.21	1.18883	
326	chromodomain y-like protein 2. [source:refseq;acc:nm_152342]	0	3053.31	2799.81	1.09054	
327	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [source:refseq;acc:nm_016355]	0	175.644	161.091	1.09034	
327	septin 10 isoform 1. [source:refseq;acc:nm_144710]	1	16067.4	19094.4	1.18839	
328	60s ribosomal protein l12. [source:swissprot;acc:p30050]	0	1657.78	1805.05	1.08884	
328	brain protein 44. [source:swissprot;acc:o95563]	1	15999.1	19007.1	1.18801	
329	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [source:sptrembl;acc:q9nq02]	0	1658.07	1805.36	1.08883	
329	septin 7 (cdc10 protein homolog). [source:swissprot;acc:q16181]	1	15999.1	19007.1	1.18801	
330	60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	0	1658.23	1805.52	1.08882	
330	septin 6. [source:swissprot;acc:q14141]	1	15959.9	18957.1	1.1878	
331	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [source:swissprot;acc:p08107]	0	4088	4451	1.0888	
331	pre-mrna cleavage complex ii protein pcf11 (fragment). [source:swissprot;acc:o94913]	1	20287.2	17083.8	1.18751	
332	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [source:swissprot;acc:q9nyg5]	0	15411.3	14167	1.08783	
332	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	1	5051.16	5975.51	1.183	
333	nuclear matrix protein nmp200 related to splicing factor prp19. [source:refseq;acc:nm_014502]	1	5039.63	5961.83	1.18299	
333	poly (adp-ribose) glycohydrolase. [source:refseq;acc:nm_003631]	0	634.305	584.237	1.0857	
334	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [source:swissprot;acc:o75521]	0	3161.12	2924.8	1.0808	
334	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]	1	14924.4	17655.2	1.18298	
335	germ cell-less. [source:refseq;acc:nm_022471]	0	1829.81	1694.05	1.08014	
335	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [source:swissprot;acc:q9ny93]	1	3494.31	4129.6	1.18181	
336	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [source:sptrembl;acc:q9h5b6]	0	1766.66	1908.13	1.08008	
336	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	1	3751.3	4431.34	1.18128	
337	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [source:swissprot;acc:o15143]	0	2039.07	2194.52	1.07624	
337	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	1	20446.1	24136.4	1.18049	
338	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	1	20446.1	24136.4	1.18049	
338	lamin b2. [source:swissprot;acc:q03252]	0	579.262	538.704	1.07529	
339	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [source:swissprot;acc:p23378]	0	996.883	1070.03	1.07338	
339	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	1	20446.1	24136.4	1.18049	
340	dystrobrevin binding protein 1; dysbindin. [source:refseq;acc:nm_032122]	0	559.333	600	1.07271	

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/