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

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Showing element 1564 to 1613 of 3228 in total

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

Rank	description	red	green	network_comparison
1564	atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047]	218.277	214.739	1.01648
1565	eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5]	221.128	224.767	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	r3h domain protein 1. [swissprot;acc:q15032]	218.105	214.573
1574	tata element modulatory factor (tmf). [swissprot;acc:p82094]	222.585	218.982	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	cda11 protein. [refseq;acc:nm_032026]	213.181	209.732	1.01644
1580	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	168.018	170.769	1.01637
1581	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	168.002	170.753
1582	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	168.098	170.844	1.01634
1583	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	168.091	170.837
1584	6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336]	216.891	220.432	1.01633
1585	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	168.145	170.888	1.01631
1586	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	225.79
1587	protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312]	220.129	216.598	1.0163
1588	ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1]	177.834	180.725	1.01626
1589	valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640]	223.589	227.219	1.01624
1590	thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818]	225.119	228.769	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	adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843]	222.133	225.731	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	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	217.871	214.404	1.01617
1600	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	225.675	1.01608
1601	phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305]	217.268	213.842	1.01602
1602	phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871]	217.334	213.914	1.01599
1603	heat shock factor binding protein 1. [swissprot;acc:o75506]	216.62	213.22	1.01595
1604	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760]	214.984	211.614	1.01593
1605	hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317]	217.322	213.916	1.01592
1606	apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772]	207.916	204.662	1.0159
1607	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761]	214.982	211.622	1.01588
1608	ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349]	208.106	204.867	1.01581
1609	utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851]	208.113	204.876	1.0158
1610	ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350]	208.122	204.886	1.01579
1611	p10-binding protein. [refseq;acc:nm_024491]	221.313	217.877	1.01577
1612	enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666]	221.426	224.902	1.0157
1613	hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410]	182.378	185.241

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.