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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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

Results: HTML CSV LaTeX

Showing element 3180 to 3229 of 6456 in total

Interaction Map  : High confidence
Value Type  : Ranked
Filtered  : 1

Rank	Hugo	Network Comparison Type	description	red	network_comparison	green
1590	TYMS	Divided	thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818]	225.119	1.01621	228.769
1591	no value		dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
	PMM2	Subtracted	phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305]	217.268	3.426	213.842
1592	GTF2B		transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403]	228.611		225.185
	SDF2	Divided	stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470]	225.119	1.01621	228.769
1593	SDF2L1		stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8]
	ZNHIT3	Subtracted	thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649]	228.611	3.426	225.185
1594	JPH4	Divided	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	225.731
	NHP2L1	Subtracted	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]	228.611	3.426	225.185
1595	no value	Divided	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	225.731
	NUFIP1	Subtracted	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]	228.611	3.426	225.185
1596	AP1G1	Divided	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]	222.134	1.01619	225.731
	PMM1	Subtracted	phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871]	217.334	3.42	213.914
1597	AP1S3	Divided	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]	222.134	1.01619	225.731
	FOXA1	Subtracted	hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317]	217.322	3.406	213.916
1598	no value		heat shock factor binding protein 1. [swissprot;acc:o75506]	216.62	3.4	213.22
	AP1S1	Divided	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]	222.134	1.01619	225.731
1599	CLK2	Subtracted	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760]	214.984	3.37	211.614
	DTNBP1	Divided	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	217.871	1.01617	214.404
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	1.01608	225.675
	CLK3	Subtracted	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761]	214.982	3.36	211.622
1601	PMM2	Divided	phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305]	217.268	1.01602	213.842
	SHMT1	Subtracted	serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896]	221.045	3.346	217.699
1602	FOXA2		hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261]	217.233	3.336	213.897
	PMM1	Divided	phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871]	217.334	1.01599	213.914
1603	no value		heat shock factor binding protein 1. [swissprot;acc:o75506]	216.62	1.01595	213.22
	EEA1	Subtracted	early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566]	228.654	3.279	231.933
1604	BUB3		mitotic checkpoint protein bub3. [swissprot;acc:o43684]	221.934	3.276	218.658
	CLK2	Divided	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760]	214.984	1.01593	211.614
1605	FOXA1		hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317]	217.322	1.01592	213.916
	ZNF207	Subtracted	zinc finger protein 207. [swissprot;acc:o43670]	221.934	3.276	218.658
1606	APOA1BP	Divided	apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772]	207.916	1.0159	204.662
	MORF4L2	Subtracted	transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014]	228.477	3.27	231.747
1607	no value		transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]	228.484	3.256	231.74
	CLK3	Divided	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761]	214.982	1.01588	211.622
1608	GSPT1	Subtracted	g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170]	218.789	3.256	215.533
	TMEM189	Divided	ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349]	208.106	1.01581	204.867
1609	APOA1BP	Subtracted	apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772]	207.916	3.254	204.662
	UGP2	Divided	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	204.876
1610	RPUSD2	Subtracted	c18b11 homolog (44.9kd). [refseq;acc:nm_152260]	217.446	3.246	214.2
	UBE2V2	Divided	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	204.886
1611	CEP70		p10-binding protein. [refseq;acc:nm_024491]	221.313	1.01577	217.877
	TMBIM4	Subtracted	z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24]	217.446	3.246	214.2
1612	no value	Divided	enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666]	221.426	1.0157	224.902
	TMBIM1	Subtracted	pp1201 protein. [refseq;acc:nm_022152]	217.446	3.246	214.2
1613	FAIM2		lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]
	HTATIP2	Divided	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	1.0157	185.241
1614	no value	Subtracted	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]	217.446	3.246	214.2
	FOXA2	Divided	hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261]	217.233	1.0156	213.897
1615	POLE2		dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282]	246.38		242.596

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.