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.

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

Results: HTML CSV LaTeX

Showing element 1600 to 1649 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
800	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [source:swissprot;acc:q15406]	Divided	6075.55	6746.92	1.1105	
801	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [source:swissprot;acc:o00505]	Divided	6456.35	7169.75	1.1105	
801	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	Subtracted	779.167	1390.33	611.163	
802	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [source:swissprot;acc:q12873]	Subtracted	779.167	1390.33	611.163	
802	target of egr1, member 1 (nuclear); target of egr1, member 1. [source:refseq;acc:nm_025077]	Divided	6455.66	7168.82	1.11047	
803	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	Subtracted	779.167	1390.33	611.163	
803	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [source:swissprot;acc:o00629]	Divided	6455.02	7167.96	1.11045	
804	nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [source:swissprot;acc:q9y6m9]	Divided	6770.78	7517.97	1.11036	
804	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	Subtracted	779.167	1390.33	611.163	
805	60s ribosomal protein l39. [source:swissprot;acc:p02404]	Divided	4708.61	5226.71	1.11003	
805	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	Subtracted	779.167	1390.33	611.163	
806	60s ribosomal protein l18a. [source:swissprot;acc:q02543]	Divided	4708.61	5226.71	1.11003	
806	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	Subtracted	779.167	1390.33	611.163	
807	40s ribosomal protein s19. [source:swissprot;acc:p39019]	Divided	4708.61	5226.71	1.11003	
807	chromodomain helicase dna binding protein 5. [source:refseq;acc:nm_015557]	Subtracted	779.167	1390.33	611.163	
808	60s ribosomal protein l31. [source:swissprot;acc:p12947]	Divided	4708.61	5226.71	1.11003	
808	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [source:swissprot;acc:o14519]	Subtracted	779.167	1390.33	611.163	
809	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [source:swissprot;acc:p49760]	Subtracted	6435.94	7045.75	609.81	
809	wd-repeat protein 3. [source:swissprot;acc:q9unx4]	Divided	4039.81	4484.22	1.11001	
810	jm1 protein. [source:refseq;acc:nm_014008]	Divided	5794.8	6427.79	1.10923	
810	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [source:swissprot;acc:p49761]	Subtracted	6435.02	7044.65	609.63	
811	adiponectin receptor 2. [source:refseq;acc:nm_024551]	Subtracted	3153.1	3762.56	609.46	
811	atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p30049]	Divided	6000.07	6655.11	1.10917	
812	puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [source:swissprot;acc:p55786]	Subtracted	5745.61	6354.75	609.14	
812	target of myb protein 1. [source:swissprot;acc:o60784]	Divided	5640.79	6255.85	1.10904	
813	huntingtin-associated protein-interacting protein (duo protein). [source:swissprot;acc:o60229]	Divided	5641.11	6255.99	1.109	
813	leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [source:swissprot;acc:p09960]	Subtracted	5745.61	6354.75	609.14	
814	dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [source:swissprot;acc:q02127]	Subtracted	5745.61	6354.75	609.14	
814	triple functional domain protein (ptprf interacting protein). [source:swissprot;acc:o75962]	Divided	5641.12	6255.99	1.109	
815	midasin (midas-containing protein). [source:swissprot;acc:q9nu22]	Divided	4483.08	4971.62	1.10897	
815	poly (adp-ribose) glycohydrolase. [source:refseq;acc:nm_003631]	Subtracted	5786.67	6395.78	609.11	
816	mto1 protein homolog (cgi-02). [source:swissprot;acc:q9y2z2]	Subtracted	5786.67	6395.78	609.11	
816	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [source:refseq;acc:nm_144678]	Divided	5641.53	6256.17	1.10895	
817	atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p36542]	Subtracted	5657.53	6263.02	605.49	
817	ornithine decarboxylase (ec 4.1.1.17) (odc). [source:swissprot;acc:p11926]	Divided	6811.2	7547.35	1.10808	
818	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [source:refseq;acc:nm_005763]	Divided	6807.78	7543.28	1.10804	
818	atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [source:swissprot;acc:p48047]	Subtracted	5657.53	6263.02	605.49	
819	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [source:swissprot;acc:p56559]	Subtracted	5912.84	6517.69	604.85	
819	ornithine decarboxylase antizyme inhibitor. [source:swissprot;acc:o14977]	Divided	6805.45	7540.5	1.10801	
820	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [source:swissprot;acc:q96a70]	Divided	6805.86	7540.99	1.10801	
820	vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [source:swissprot;acc:p12953]	Subtracted	5912.84	6517.69	604.85	
821	adp-ribosylation factor-like protein 4. [source:swissprot;acc:p40617]	Subtracted	5912.84	6517.69	604.85	
821	trna isopentenylpyrophosphate transferase. [source:refseq;acc:nm_017646]	Divided	6257.99	6932.95	1.10786	
822	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	Subtracted	4811.02	5414.64	603.62	
822	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [source:swissprot;acc:q08999]	Divided	6311.6	6989.33	1.10738	
823	atpase inhibitor, mitochondrial precursor. [source:swissprot;acc:q9uii2]	Subtracted	4810.85	5414.23	603.38	
823	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [source:swissprot;acc:p28749]	Divided	6311.83	6989.6	1.10738	
824	atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p36542]	Divided	5657.53	6263.02	1.10702	
824	polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [source:refseq;acc:nm_019025]	Subtracted	4810.85	5414.23	603.38	
825	atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [source:swissprot;acc:p48047]	Divided	5657.53	6263.02	1.10702	

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/