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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1575 to 1624 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
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. [source:refseq;acc:nm_020680]	222.585	218.982	1.01645	
1576	NUP98	nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [source:swissprot;acc:p52948]	222.585	218.982	1.01645	
1577	AMMECR1	ammecr1 protein. [source:refseq;acc:nm_015365]	222.585	218.982	1.01645	
1578	RAE1	mrna-associated protein mrnp 41 (rae1 protein homolog). [source:swissprot;acc:p78406]	222.585	218.982	1.01645	
1579	TATDN1	cda11 protein. [source:refseq;acc:nm_032026]	213.181	209.732	1.01644	
1580	CCNB2	g2/mitotic-specific cyclin b2. [source:swissprot;acc:o95067]	168.018	170.769	1.01637	
1581	CDK3	cell division protein kinase 3 (ec 2.7.1.-). [source:swissprot;acc:q00526]	168.002	170.753	1.01637	
1582	CCNB1	g2/mitotic-specific cyclin b1. [source:swissprot;acc:p14635]	168.098	170.844	1.01634	
1583	CDK2	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [source:swissprot;acc:p24941]	168.091	170.837	1.01634	
1584	PGLS	6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [source: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). [source: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). [source:swissprot;acc:q10567]	222.166	225.79	1.01631	
1587	C20orf4	protein c20orf4 (protein cgi-23) (pro0225). [source:swissprot;acc:q9y312]	220.129	216.598	1.0163	
1588	RNF25	ring finger protein 25 (ec 6.3.2.-). [source: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). [source:swissprot;acc:p26640]	223.589	227.219	1.01624	
1590	TYMS	thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [source:swissprot;acc:p04818]	225.119	228.769	1.01621	
1591		dihydrofolate reductase (ec 1.5.1.3). [source:swissprot;acc:p00374]	225.119	228.769	1.01621	
1592	SDF2	stromal cell-derived factor 2 precursor (sdf-2). [source:swissprot;acc:q99470]	225.119	228.769	1.01621	
1593	SDF2L1	stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [source:swissprot;acc:q9hcn8]	225.119	228.769	1.01621	
1594	JPH4	adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [source: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). [source:swissprot;acc:p56377]	222.134	225.731	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). [source:swissprot;acc:o43747]	222.134	225.731	1.01619	
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). [source:swissprot;acc:q96pc3]	222.134	225.731	1.01619	
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). [source:swissprot;acc:q00382]	222.134	225.731	1.01619	
1599	DTNBP1	dystrobrevin binding protein 1; dysbindin. [source: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). [source:swissprot;acc:p21851]	222.103	225.675	1.01608	
1601	PMM2	phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [source:swissprot;acc:o15305]	217.268	213.842	1.01602	
1602	PMM1	phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [source:swissprot;acc:q92871]	217.334	213.914	1.01599	
1603		heat shock factor binding protein 1. [source:swissprot;acc:o75506]	216.62	213.22	1.01595	
1604	CLK2	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [source:swissprot;acc:p49760]	214.984	211.614	1.01593	
1605	FOXA1	hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [source:swissprot;acc:p55317]	217.322	213.916	1.01592	
1606	APOA1BP	apolipoprotein a-i binding protein; apoa-i binding protein. [source:refseq;acc:nm_144772]	207.916	204.662	1.0159	
1607	CLK3	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [source:swissprot;acc:p49761]	214.982	211.622	1.01588	
1608	TMEM189	ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [source:refseq;acc:nm_003349]	208.106	204.867	1.01581	
1609	UGP2	utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [source:swissprot;acc:q16851]	208.113	204.876	1.0158	
1610	UBE2V2	ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [source:refseq;acc:nm_003350]	208.122	204.886	1.01579	
1611	CEP70	p10-binding protein. [source:refseq;acc:nm_024491]	221.313	217.877	1.01577	
1612		enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [source:refseq;acc:nm_014666]	221.426	224.902	1.0157	
1613	HTATIP2	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. [source:refseq;acc:nm_006410]	182.378	185.241	1.0157	
1614	FOXA2	hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [source:swissprot;acc:q9y261]	217.233	213.897	1.0156	
1615	POLE2	dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [source:swissprot;acc:p56282]	246.38	242.596	1.0156	
1616	NAGS	n-acetylglutamate synthase. [source:refseq;acc:nm_153006]	223.179	226.611	1.01538	
1617	SHMT1	serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [source:swissprot;acc:p34896]	221.045	217.699	1.01537	
1618	TCEA2	transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [source:swissprot;acc:q15560]	227.768	231.246	1.01527	
1619		transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [source:swissprot;acc:p23193]	227.768	231.246	1.01527	
1620	GTF2B	transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [source:swissprot;acc:q00403]	228.611	225.185	1.01521	
1621	ZNHIT3	thyroid receptor interacting protein 3 (trip-3) (fragment). [source:swissprot;acc:q15649]	228.611	225.185	1.01521	
1622	NHP2L1	nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [source:swissprot;acc:p55769]	228.611	225.185	1.01521	
1623	NUFIP1	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. [source:refseq;acc:nm_012345]	228.611	225.185	1.01521	
1624	PDCD11	rrp5 protein homolog (programmed cell death protein 11). [source:swissprot;acc:q14690]	230.643	227.194	1.01518	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/