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 green red network_comparison
Results: HTML CSV LaTeX Showing element 1675 to 1724 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	green	red	network_comparison	
1675	probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [source:swissprot;acc:q9uhi6]	231.729	228.496	1.01415	
1676	importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [source:swissprot;acc:q92973]	215.645	218.691	1.01413	
1677	glutathione s-transferase p (ec 2.5.1.18) (gst class-pi) (gstp1-1). [source:swissprot;acc:p09211]	221.732	218.654	1.01408	
1678	serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [source:swissprot;acc:q9upe1]	213.889	216.899	1.01407	
1679	gtp binding protein 2. [source:refseq;acc:nm_019096]	213.889	216.899	1.01407	
1680	cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [source:swissprot;acc:q99941]	213.889	216.899	1.01407	
1681	dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [source:refseq;acc:nm_012135]	213.889	216.899	1.01407	
1682	sfrs protein kinase 2 isoform b. [source:refseq;acc:nm_182691]	213.889	216.899	1.01407	
1683	cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [source:swissprot;acc:p18850]	213.889	216.899	1.01407	
1684	sfrs protein kinase 1; sr protein kinase 1. [source:refseq;acc:nm_003137]	213.889	216.899	1.01407	
1685	xap-5 protein (hxc-26 protein). [source:swissprot;acc:q14320]	213.889	216.899	1.01407	
1686	putative sialoglycoprotease type 2. [source:refseq;acc:nm_022353]	217.704	220.75	1.01399	
1687	atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p30049]	212.386	215.345	1.01393	
1688	transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [source:swissprot;acc:q9ubu8]	231.703	228.523	1.01392	
1689	dead-box protein 4 (vasa homolog). [source:swissprot;acc:q9nqi0]	225.163	228.277	1.01383	
1690	40s ribosomal protein s24 (s19). [source:swissprot;acc:p16632]	227.184	224.091	1.0138	
1691	translation initiation factor if-2. [source:swissprot;acc:o60841]	214.315	217.263	1.01376	
1692	rna-binding protein 9 (rna binding motif protein 9) (hexaribonucleotide binding protein 2) (repressor of tamoxifen transcriptional activity). [source:swissprot;acc:o43251]	215.551	218.515	1.01375	
1693	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [source:swissprot;acc:p12268]	215.971	218.937	1.01373	
1694	gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [source:swissprot;acc:p49915]	215.971	218.937	1.01373	
1695	inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [source:swissprot;acc:p20839]	215.971	218.937	1.01373	
1696	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [source:swissprot;acc:q9h361]	214.69	217.624	1.01367	
1697	hskin17 protein. [source:refseq;acc:nm_012311]	214.69	217.624	1.01367	
1698	carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [source:swissprot;acc:p43155]	214.69	217.624	1.01367	
1699	polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [source:swissprot;acc:q13310]	214.69	217.624	1.01367	
1700	polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [source:swissprot;acc:p11940]	214.69	217.624	1.01367	
1701	glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [source:swissprot;acc:p11413]	219.024	216.079	1.01363	
1702	dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [source:swissprot;acc:o43542]	219.024	216.079	1.01363	
1703	atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [source:swissprot;acc:o94762]	219.024	216.079	1.01363	
1704	ataxin 2-binding protein. [source:swissprot;acc:q9nwb1]	215.577	218.514	1.01362	
1705	serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [source:swissprot;acc:p33172]	220.847	223.846	1.01358	
1706	immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [source:swissprot;acc:p78318]	220.847	223.846	1.01358	
1707	mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [source:swissprot;acc:o60566]	218.334	221.283	1.01351	
1708	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	218.334	221.283	1.01351	
1709	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [source:swissprot;acc:q03014]	195.385	198.014	1.01346	
1710	casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [source:swissprot;acc:p49674]	224.21	227.225	1.01345	
1711	biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [source:swissprot;acc:p50747]	215.553	218.436	1.01337	
1712	transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [source:swissprot;acc:q15544]	211.375	208.598	1.01331	
1713	sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [source:swissprot;acc:q99963]	204.111	206.823	1.01329	
1714	armet protein precursor (arginine-rich protein). [source:swissprot;acc:p55145]	203.844	206.549	1.01327	
1715	histidine decarboxylase (ec 4.1.1.22) (hdc). [source:swissprot;acc:p19113]	203.844	206.549	1.01327	
1716	sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [source:swissprot;acc:q99962]	203.818	206.522	1.01327	
1717	o-sialoglycoprotein endopeptidase. [source:refseq;acc:nm_017807]	218.164	221.058	1.01327	
1718	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [source:swissprot;acc:q99961]	203.553	206.251	1.01325	
1719	helicase (fragment). [source:sptrembl;acc:q92771]	189.679	187.204	1.01322	
1720	dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [source:refseq;acc:nm_030655]	189.679	187.205	1.01322	
1721	casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [source:swissprot;acc:p48730]	224.164	227.125	1.01321	
1722	40s ribosomal protein s13. [source:swissprot;acc:q02546]	223.813	220.899	1.01319	
1723	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [source:swissprot;acc:o95544]	215.147	212.36	1.01312	
1724	inositol polyphosphate multikinase. [source:refseq;acc:nm_152230]	220.53	217.676	1.01311	

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/