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 1577 to 1626 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1577	26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [source:swissprot;acc:q92524]	5923.66	6349.04	1.07181	
1578	proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [source:swissprot;acc:p25789]	6213.27	6659.39	1.0718	
1579	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	5842.44	6261.87	1.07179	
1580	glycogenin-1 (ec 2.4.1.186). [source:swissprot;acc:p46976]	6376.12	6833.59	1.07175	
1581	adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [source:swissprot;acc:p55263]	6376.12	6833.59	1.07175	
1582	protein x 0001. [source:refseq;acc:nm_016302]	6376.12	6833.59	1.07175	
1583	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [source:swissprot;acc:o15488]	6376.12	6833.59	1.07175	
1584	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [source:swissprot;acc:p23378]	5933.25	6358.78	1.07172	
1585	26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [source:swissprot;acc:q9unm6]	5858.48	6278.32	1.07166	
1586	ubiquitin-like protein smt3c precursor (ubiquitin-homology domain protein pic1) (ubiquitin-like protein ubl1) (ubiquitin-related protein sumo-1) (gap modifying protein 1) (gmp1) (sentrin). [source:swissprot;acc:q93068]	5784.36	6198.73	1.07164	
1587	udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [source:swissprot;acc:o60701]	5784.36	6198.73	1.07164	
1588	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	3600.99	3360.33	1.07162	
1589	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	3600.99	3360.33	1.07162	
1590	fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [source:refseq;acc:nm_014281]	6364.01	6819.38	1.07155	
1591	multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [source:swissprot;acc:q13155]	6364.01	6819.38	1.07155	
1592	26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [source:swissprot;acc:o00231]	5853.1	6271.79	1.07153	
1593	proliferating cell nuclear antigen (pcna) (cyclin). [source:swissprot;acc:p12004]	4977.77	5333.78	1.07152	
1594	transportin-sr; importin 12. [source:refseq;acc:nm_012470]	5184.94	5555.76	1.07152	
1595	proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [source:swissprot;acc:p28062]	6351.32	6805.39	1.07149	
1596	enigma protein; lim domain protein. [source:refseq;acc:nm_005451]	5665.34	6070.32	1.07148	
1597	eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [source:swissprot;acc:o15371]	5665.34	6070.32	1.07148	
1598	lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [source:swissprot;acc:p36776]	5068.17	5430.41	1.07147	
1599	40s ribosomal protein s24 (s19). [source:swissprot;acc:p16632]	5184.45	5554.97	1.07147	
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	

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/