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 2951 to 3000 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1476	ran-gtp binding protein (fragment). [source:sptrembl;acc:o60518]	Divided	218.591	214.457	1.01928	
1476	reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [source:swissprot;acc:o75298]	Subtracted	207.022	211.073	4.051	
1477	reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [source:swissprot;acc:o95197]	Subtracted	207.013	211.05	4.037	
1477	transformer-2 protein homolog (tra-2 alpha). [source:swissprot;acc:q13595]	Divided	215.328	211.267	1.01922	
1478	arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [source:swissprot;acc:q15815]	Divided	215.122	211.066	1.01922	
1478	thyroid receptor interacting protein 12 (trip12). [source:swissprot;acc:q14669]	Subtracted	205.817	209.851	4.034	
1479	dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [source:swissprot;acc:p36957]	Subtracted	205.817	209.851	4.034	
1479	maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [source:swissprot;acc:q9nzw5]	Divided	228.469	232.855	1.0192	
1480	cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [source:refseq;acc:nm_007007]	Divided	218.664	214.55	1.01918	
1480	mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [source:swissprot;acc:o43318]	Subtracted	213.251	209.264	3.987	
1481	alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [source:swissprot;acc:p42024]	Subtracted	225.148	221.177	3.971	
1481	cell division cycle protein 23; anaphase-promoting complex subunit 8. [source:refseq;acc:nm_004661]	Divided	208.432	204.516	1.01915	
1482	beta-centractin (actin-related protein 1b) (arp1b). [source:swissprot;acc:p42025]	Subtracted	225.148	221.177	3.971	
1482	limbic system-associated membrane protein precursor (lsamp). [source:swissprot;acc:q13449]	Divided	224.354	220.15	1.0191	
1483	pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [source:swissprot;acc:p11177]	Divided	198.927	202.726	1.0191	
1483	rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [source:swissprot;acc:p98175]	Subtracted	228.419	232.376	3.957	
1484	2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [source:swissprot;acc:p12694]	Divided	198.927	202.726	1.0191	
1484	cytochrome c. [source:swissprot;acc:p00001]	Subtracted	228.419	232.376	3.957	
1485	heparan sulfate 6-o-sulfotransferase 2. [source:refseq;acc:nm_147174]	Subtracted	228.419	232.376	3.957	
1485	j kappa-recombination signal binding protein (rbp-j kappa). [source:swissprot;acc:q06330]	Divided	207.877	203.989	1.01906	
1486	heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [source:refseq;acc:nm_004807]	Subtracted	228.419	232.376	3.957	
1486	human immunodeficiency virus type i enhancer binding protein 3. [source:refseq;acc:nm_024503]	Divided	207.877	203.989	1.01906	
1487	fatty acid hydroxylase domain containing 1. [source:refseq;acc:nm_024306]	Subtracted	228.419	232.376	3.957	
1487	zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [source:swissprot;acc:p15822]	Divided	207.877	203.989	1.01906	
1488	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [source:swissprot;acc:p31629]	Divided	207.877	203.989	1.01906	
1488	ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [source:refseq;acc:nm_016312]	Subtracted	228.419	232.376	3.957	
1489	elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [source:refseq;acc:nm_018127]	Subtracted	228.419	232.376	3.957	
1489	mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [source:swissprot;acc:o43318]	Divided	213.251	209.264	1.01905	
1490	protein cgi-147. [source:swissprot;acc:q9y3e5]	Divided	221.961	226.186	1.01903	
1490	rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [source:swissprot;acc:p52756]	Subtracted	228.419	232.376	3.957	
1491	glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [source:swissprot;acc:p06744]	Divided	217.704	221.839	1.01899	
1491	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	Subtracted	116.71	120.654	3.944	
1492	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	Subtracted	116.771	120.707	3.936	
1492	opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [source:swissprot;acc:q14982]	Divided	224.159	220.017	1.01883	
1493	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [source:swissprot;acc:p29803]	Divided	204.146	207.988	1.01882	
1493	uridine kinase-like 1. [source:swissprot;acc:q9nwz5]	Subtracted	218.084	214.149	3.935	
1494	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [source:swissprot;acc:q9bwt3]	Subtracted	116.845	120.772	3.927	
1494	pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [source:swissprot;acc:p08559]	Divided	204.133	207.967	1.01878	
1495	casein kinase i alpha s-like. [source:refseq;acc:nm_145203]	Divided	229.459	225.237	1.01874	
1495	cell division cycle protein 23; anaphase-promoting complex subunit 8. [source:refseq;acc:nm_004661]	Subtracted	208.432	204.516	3.916	
1496	casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [source:swissprot;acc:p48729]	Divided	229.459	225.237	1.01874	
1496	kinesin family member c3. [source:refseq;acc:nm_005550]	Subtracted	214.727	210.838	3.889	
1497	exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [source:refseq;acc:nm_003400]	Divided	224.476	220.363	1.01866	
1497	j kappa-recombination signal binding protein (rbp-j kappa). [source:swissprot;acc:q06330]	Subtracted	207.877	203.989	3.888	
1498	human immunodeficiency virus type i enhancer binding protein 3. [source:refseq;acc:nm_024503]	Subtracted	207.877	203.989	3.888	
1498	neurotrimin precursor (hnt). [source:swissprot;acc:q9p121]	Divided	224.022	219.924	1.01863	
1499	transcription factor smif; decapping enzyme hdcp1a. [source:refseq;acc:nm_018403]	Divided	224.509	220.411	1.01859	
1499	zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [source:swissprot;acc:p15822]	Subtracted	207.877	203.989	3.888	
1500	cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [source:refseq;acc:nm_016129]	Divided	213.398	209.52	1.01851	
1500	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [source:swissprot;acc:p31629]	Subtracted	207.877	203.989	3.888	

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/