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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2113 to 2162 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
529	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [source:swissprot;acc:q9nvp1]	Ranked	251.653	235.506	1.06856	
529	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [source:swissprot;acc:q15388]	Measured	8600.02	9792.49	1.13866	
529	nucleolar protein nop56 (nucleolar protein 5a). [source:swissprot;acc:o00567]	Rooted	50.3239	54.6658	1.08628	
529	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [source:swissprot;acc:q9y289]	Squared	28990.9	34656.4	1.19542	
530	40s ribosomal protein s14 (pro2640). [source:swissprot;acc:p06366]	Rooted	50.6537	46.6413	1.08603	
530	monoglyceride lipase; lysophospholipase-like. [source:refseq;acc:nm_007283]	Squared	27179.5	32490.8	1.19542	
530	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [source:swissprot;acc:p40855]	Measured	8600.02	9792.49	1.13866	
530	u6 snrna-associated sm-like protein lsm6 (sm protein f). [source:swissprot;acc:q9y4y8]	Ranked	227.483	212.994	1.06803	
531	40s ribosomal protein s18 (ke-3) (ke3). [source:swissprot;acc:p25232]	Rooted	50.6537	46.6413	1.08603	
531	nuclear matrix protein nmp200 related to splicing factor prp19. [source:refseq;acc:nm_014502]	Ranked	223.356	209.149	1.06793	
531	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [source:refseq;acc:nm_145913]	Squared	28980.7	34643.6	1.1954	
531	transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [source:swissprot;acc:q00403]	Measured	4651.88	5296.78	1.13863	
532	kidney and liver proline oxidase 1. [source:refseq;acc:nm_021232]	Squared	28967	34626.4	1.19537	
532	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [source:swissprot;acc:o43236]	Rooted	107.961	117.197	1.08555	
532	thyroid receptor interacting protein 3 (trip-3) (fragment). [source:swissprot;acc:q15649]	Measured	4651.88	5296.78	1.13863	
532	zinc finger-like protein 9. [source:refseq;acc:nm_033414]	Ranked	250.942	235.004	1.06782	
533	60s ribosomal protein l13, mitochondrial (l13mt). [source:swissprot;acc:q9byd1]	Rooted	50.8036	46.8198	1.08509	
533	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [source:swissprot;acc:q9umx9]	Ranked	250.942	235.004	1.06782	
533	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]	Measured	4651.88	5296.78	1.13863	
533	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [source:swissprot;acc:q92911]	Squared	28937.1	34588.8	1.19531	
534	40s ribosomal protein s16. [source:swissprot;acc:p17008]	Rooted	50.8036	46.8198	1.08509	
534	dehydrodolichyl diphosphate synthase. [source:refseq;acc:nm_024887]	Squared	27034.1	32301.8	1.19485	
534	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [source:swissprot;acc:p36915]	Ranked	250.942	235.004	1.06782	
534	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]	Measured	4651.88	5296.78	1.13863	
535	60s ribosomal protein l13a (23 kda highly basic protein). [source:swissprot;acc:p40429]	Rooted	50.8041	46.8218	1.08505	
535	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [source:swissprot;acc:p52434]	Ranked	236.662	252.708	1.0678	
535	maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [source:swissprot;acc:q13368]	Squared	37147.5	44372.1	1.19448	
535	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [source:swissprot;acc:p51571]	Measured	10603.5	12069.5	1.13826	
536	calsyntenin-1 precursor. [source:swissprot;acc:o94985]	Measured	10603.5	12069.5	1.13826	
536	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [source:swissprot;acc:p31260]	Rooted	66.0815	71.6562	1.08436	
536	integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [source:swissprot;acc:q9y287]	Squared	28657.6	34208.6	1.1937	
536	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [source:swissprot;acc:p05455]	Ranked	242.531	227.136	1.06778	
537	homeobox protein hox-b9 (hox-2e) (hox-2.5). [source:swissprot;acc:p17482]	Rooted	66.0817	71.6545	1.08433	
537	integral membrane protein 2c (transmembrane protein bri3) (npd018). [source:swissprot;acc:q9nqx7]	Squared	28657.6	34208.6	1.1937	
537	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [source:swissprot;acc:o43143]	Ranked	229.803	215.301	1.06736	
537	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [source:swissprot;acc:o14521]	Measured	10603.5	12069.5	1.13826	
538	dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [source:swissprot;acc:p52436]	Ranked	237.627	253.604	1.06724	
538	homeobox protein hox-a9 (hox-1g). [source:swissprot;acc:p31269]	Rooted	66.0817	71.6543	1.08433	
538	integral membrane protein 2a (e25 protein). [source:swissprot;acc:o43736]	Squared	28657.6	34208.6	1.1937	
538	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [source:swissprot;acc:p23467]	Measured	10603.5	12069.4	1.13825	
539	homeobox protein hox-c9 (hox-3b). [source:swissprot;acc:p31274]	Rooted	66.0818	71.6537	1.08432	
539	protein cgi-27 (c21orf19-like protein). [source:swissprot;acc:q9y316]	Ranked	236.964	252.86	1.06708	
539	thymus-specific serine protease precursor (ec 3.4.-.-). [source:swissprot;acc:q9nqe7]	Measured	10603.5	12069.4	1.13825	
539	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [source:refseq;acc:nm_020135]	Squared	20613.1	24595.9	1.19322	
540	argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [source:swissprot;acc:p04424]	Squared	26048.6	31057.4	1.19229	
540	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q99928]	Rooted	66.082	71.6526	1.0843	
540	gk001 protein. [source:refseq;acc:nm_020198]	Measured	10603.5	12069.4	1.13825	
540	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	Ranked	222.156	208.201	1.06703	
541	calsyntenin-2 precursor. [source:swissprot;acc:q9h4d0]	Measured	10600.3	12065.2	1.13819	
541	coatomer beta subunit (beta-coat protein) (beta-cop). [source:swissprot;acc:p53618]	Squared	53774.6	45105.5	1.1922	

Legend:
- Rank is the rank after comparing the two networks
- 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/