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

Results: HTML CSV LaTeX

Showing element 1580 to 1629 of 3228 in total

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

Rank	green	description	red	network_comparison
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
1608	204.867	ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349]	208.106	1.01581
1609	204.876	utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851]	208.113	1.0158
1610	204.886	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	1.01579
1611	217.877	p10-binding protein. [refseq;acc:nm_024491]	221.313	1.01577
1612	224.902	enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666]	221.426	1.0157
1613	185.241	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
1614	213.897	hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261]	217.233	1.0156
1615	242.596	dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282]	246.38
1616	226.611	n-acetylglutamate synthase. [refseq;acc:nm_153006]	223.179	1.01538
1617	217.699	serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896]	221.045	1.01537
1618	231.246	transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [swissprot;acc:q15560]	227.768	1.01527
1619		transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]
1620	225.185	transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403]	228.611	1.01521
1621		thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649]
1622		nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769]
1623		nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345]
1624	227.194	rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690]	230.643	1.01518
1625	214.2	c18b11 homolog (44.9kd). [refseq;acc:nm_152260]	217.446	1.01515
1626		z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24]
1627		pp1201 protein. [refseq;acc:nm_022152]
1628		lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]
1629		sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]

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.