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 1600 to 1649 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1600	14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [source:swissprot;acc:p52758]	6336.22	6788.96	1.07145	
1601	spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [source:swissprot;acc:o15020]	5232.14	5605.8	1.07142	
1602	spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [source:swissprot;acc:q01082]	5232.14	5605.8	1.07142	
1603	phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [source:swissprot;acc:o95394]	5232.14	5605.8	1.07142	
1604	malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [source:swissprot;acc:o95822]	6176.82	6617.91	1.07141	
1605	itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [source:refseq;acc:nm_031483]	6176.82	6617.91	1.07141	
1606	5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [source:swissprot;acc:q13126]	5232.99	5606.53	1.07138	
1607	putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [source:swissprot;acc:q9uet6]	5232.99	5606.53	1.07138	
1608	ubiquitin. [source:swissprot;acc:p02248]	6158.22	6597.55	1.07134	
1609	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	5826.74	6242.44	1.07134	
1610	eif-5a2 protein. [source:refseq;acc:nm_020390]	6222.4	6665.83	1.07126	
1611	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [source:swissprot;acc:q15642]	5497.73	5132.35	1.07119	
1612	eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [source:swissprot;acc:p10159]	6212.98	6655.12	1.07116	
1613	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [source:swissprot;acc:p82650]	6035.6	6464.5	1.07106	
1614	nefa-interacting nuclear protein nip30. [source:refseq;acc:nm_024946]	6035.6	6464.5	1.07106	
1615	lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [source:swissprot;acc:q8te12]	6035.6	6464.5	1.07106	
1616	mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [source:swissprot;acc:o94826]	6035.6	6464.5	1.07106	
1617	lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [source:swissprot;acc:o60663]	6035.6	6464.5	1.07106	
1618	proteasome subunit beta type 2 (ec 3.4.25.1) (proteasome component c7-i) (macropain subunit c7-i) (multicatalytic endopeptidase complex subunit c7-i). [source:swissprot;acc:p49721]	6035.6	6464.5	1.07106	
1619	adp-ribosylation factor-like protein 1. [source:swissprot;acc:p40616]	6035.6	6464.5	1.07106	
1620	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]	6296.52	6743.85	1.07104	
1621	sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [source:refseq;acc:nm_015077]	5520.36	5911.98	1.07094	
1622	phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [source:swissprot;acc:q13393]	6153.79	6589.52	1.07081	
1623	transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [source:swissprot;acc:p55072]	6449.02	6905.56	1.07079	
1624	similar to zinc finger protein 277. [source:sptrembl;acc:q8wwa6]	4102.1	4392.15	1.07071	
1625	zinc finger protein 277. [source:swissprot;acc:q9nrm2]	4102.1	4392.15	1.07071	
1626	phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [source:swissprot;acc:o14939]	6157.13	6591.53	1.07055	
1627	6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [source:swissprot;acc:o95336]	6038.46	6463.9	1.07046	
1628	glycine cleavage system h protein, mitochondrial precursor. [source:swissprot;acc:p23434]	5920.55	6337.28	1.07039	
1629	dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [source:refseq;acc:nm_014475]	6158.32	6590.99	1.07026	
1630	c-terminal binding protein 2 (ctbp2). [source:swissprot;acc:p56545]	9903.22	9253.79	1.07018	
1631	brachyury protein (t protein). [source:swissprot;acc:o15178]	6179.59	6613.15	1.07016	
1632	t-box transcription factor tbx19 (t-box protein 19). [source:swissprot;acc:o60806]	6179.59	6613.15	1.07016	
1633	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [source:refseq;acc:nm_181844]	9899.79	9251.2	1.07011	
1634	pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [source:refseq;acc:nm_015148]	9899.73	9251.16	1.07011	
1635	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [source:swissprot;acc:p41182]	9899.73	9251.16	1.07011	
1636	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [source:swissprot;acc:o43623]	9899.73	9251.16	1.07011	
1637	proteasome subunit alpha type 6 (ec 3.4.25.1) (proteasome iota chain) (macropain iota chain) (multicatalytic endopeptidase complex iota chain) (27 kda prosomal protein) (pros-27) (p27k). [source:swissprot;acc:p34062]	6112.4	6540.73	1.07008	
1638	c-terminal binding protein 1 (ctbp1). [source:swissprot;acc:q13363]	9895.77	9248.18	1.07002	
1639	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [source:swissprot;acc:o95544]	5939.71	6354.79	1.06988	
1640	adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [source:swissprot;acc:p30566]	7444.28	7964	1.06981	
1641	ba271b5.1 (similar to ribosomal protein s7). [source:sptrembl;acc:q9h1s9]	5782.92	6186.39	1.06977	
1642	40s ribosomal protein s7 (s8). [source:swissprot;acc:p23821]	5782.92	6186.39	1.06977	
1643	26s proteasome-associated pad1 homolog. [source:refseq;acc:nm_005805]	5782.92	6186.39	1.06977	
1644	apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [source:swissprot;acc:p04114]	5782.92	6186.39	1.06977	
1645	proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [source:swissprot;acc:p07332]	6079.19	6503.12	1.06973	
1646	molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [source:swissprot;acc:o96007]	6079.19	6503.12	1.06973	
1647	anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [source:refseq;acc:nm_014885]	6079.19	6503.12	1.06973	
1648	60s ribosomal protein l29 (cell surface heparin binding protein hip). [source:swissprot;acc:p47914]	6079.19	6503.12	1.06973	
1649	proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [source:swissprot;acc:p16591]	6079.19	6503.12	1.06973	

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/