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	Hugo	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 1558 to 1607 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison
1558	CTBP2	c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545]	196.171	192.977	1.01655
1559	BCL6B	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]	196.191	192.996
1560	GATAD2A	p66 alpha. [refseq;acc:nm_017660]	167.687	170.455	1.01651
1561	GATAD2B	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]
1562	no value	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]
1563	ATP5C1	atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542]	218.277	214.739	1.01648
1564	ATP5O	atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047]
1565	EIF3K	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	SLMO1	erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584]
1567	BBS7	bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824]
1568	no value	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	SLMO2	protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1]
1571	EIF3EIP	eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262]
1572	RBM7	putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]
1573	R3HDM1	r3h domain protein 1. [swissprot;acc:q15032]	218.105	214.573
1574	TMF1	tata element modulatory factor (tmf). [swissprot;acc:p82094]	222.585	218.982	1.01645
1575	SCYL1	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	NUP98	nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948]
1577	AMMECR1	ammecr1 protein. [refseq;acc:nm_015365]
1578	RAE1	mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406]
1579	TATDN1	cda11 protein. [refseq;acc:nm_032026]	213.181	209.732	1.01644
1580	CCNB2	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	168.018	170.769	1.01637
1581	CDK3	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	168.002	170.753
1582	CCNB1	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	168.098	170.844	1.01634
1583	CDK2	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	168.091	170.837
1584	PGLS	6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336]	216.891	220.432	1.01633
1585	CDC2	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	AP1B1	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	C20orf4	protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312]	220.129	216.598	1.0163
1588	RNF25	ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1]	177.834	180.725	1.01626
1589	VARS	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	TYMS	thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818]	225.119	228.769	1.01621
1591	no value	dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
1592	SDF2	stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470]
1593	SDF2L1	stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8]
1594	JPH4	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	no value	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	AP1G1	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	AP1S3	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	AP1S1	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	DTNBP1	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	217.871	214.404	1.01617
1600	AP2B1	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	PMM2	phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305]	217.268	213.842	1.01602
1602	PMM1	phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871]	217.334	213.914	1.01599
1603	no value	heat shock factor binding protein 1. [swissprot;acc:o75506]	216.62	213.22	1.01595
1604	CLK2	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760]	214.984	211.614	1.01593
1605	FOXA1	hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317]	217.322	213.916	1.01592
1606	APOA1BP	apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772]	207.916	204.662	1.0159
1607	CLK3	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761]	214.982	211.622	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
- Hugo is the HGNC identifier if it exists
- 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.