MK5 Microarray Data

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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Value Type	Gene	Rank	green	description	Network Comparison Type	Filtered	Interaction Map	red	network_comparison

Results: HTML CSV LaTeX

Showing element 1558 to 1607 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Interaction Map  : High confidence

Rank	green	description	red	network_comparison
1558	192.977	c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545]	196.171	1.01655
1559	192.996	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]	196.191
1560	170.455	p66 alpha. [refseq;acc:nm_017660]	167.687	1.01651
1561		transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]
1562		tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]
1563	214.739	atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542]	218.277	1.01648
1564		atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047]
1565	224.767	eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5]	221.128	1.01646
1566		erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584]
1567		bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824]
1568		ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]
1569		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]
1570		protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1]
1571		eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262]
1572		putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]
1573	214.573	r3h domain protein 1. [swissprot;acc:q15032]	218.105
1574	218.982	tata element modulatory factor (tmf). [swissprot;acc:p82094]	222.585	1.01645
1575		scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680]
1576		nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948]
1577		ammecr1 protein. [refseq;acc:nm_015365]
1578		mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406]
1579	209.732	cda11 protein. [refseq;acc:nm_032026]	213.181	1.01644
1580	170.769	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	168.018	1.01637
1581	170.753	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	168.002
1582	170.844	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	168.098	1.01634
1583	170.837	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	168.091
1584	220.432	6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336]	216.891	1.01633
1585	170.888	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	168.145	1.01631
1586	225.79	adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567]	222.166
1587	216.598	protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312]	220.129	1.0163
1588	180.725	ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1]	177.834	1.01626
1589	227.219	valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640]	223.589	1.01624
1590	228.769	thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818]	225.119	1.01621
1591		dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
1592		stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470]
1593		stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8]
1594	225.731	adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843]	222.133	1.0162
1595		adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]	222.134	1.01619
1596		adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [swissprot;acc:o43747]
1597		adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3]
1598		adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382]
1599	214.404	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	217.871	1.01617
1600	225.675	adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [swissprot;acc:p21851]	222.103	1.01608
1601	213.842	phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305]	217.268	1.01602
1602	213.914	phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871]	217.334	1.01599
1603	213.22	heat shock factor binding protein 1. [swissprot;acc:o75506]	216.62	1.01595
1604	211.614	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760]	214.984	1.01593
1605	213.916	hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317]	217.322	1.01592
1606	204.662	apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772]	207.916	1.0159
1607	211.622	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761]	214.982	1.01588

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.