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

Results: HTML CSV LaTeX

Showing element 501 to 550 of 77072 in total

Rank	Value Type	description	Network Comparison Type	Interaction Map	red	network_comparison	green	Filtered
16	Squared	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Subtracted	High confidence	219048	89286	129762	1
		phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]	Divided	High confidence	0.00001	7668.64	0.0766864	0
		protein kinase, lysine deficient 3. [refseq;acc:nm_020922]		Low confidence	4.89136	45.1903	221.042	0
		protein x 0004. [refseq;acc:nm_016301]		High confidence	1688.58	9.40399	179.56	1
	Rooted	cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2]	Subtracted	Low confidence	12.4097	9.7939	22.2036	0
		dystrophin. [swissprot;acc:p11532]		High confidence	17.8026	12.6757	5.12693	0
		gbp protein isoform a. [refseq;acc:nm_017870]		Low confidence	31.8923	15.8184	47.7107	1
		mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]		High confidence	203.673	21.035	182.638	1
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Divided	Low confidence	29.3087	3.84842	7.61577	0
		serpin b12. [swissprot;acc:q96p63]		High confidence	10.2928	8.67149	1.18697	0
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]		Low confidence	38.4152	1.27952	49.1529	1
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]		High confidence	51.6817	1.75117	29.5127	1
17	Measured	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	Subtracted		11223	1250	12473	0
		dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	Divided		460	2.96739	1365	1
		ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08]	Subtracted	Low confidence	4959.42	878.41	5837.83	0
		homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]		Low confidence	15464.1	2108.6	17572.7	1
		microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]		High confidence	24255.7	6086.8	18168.9
		mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Divided	Low confidence	21185	1.34491	28492
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		High confidence	859	14.8103	58	0
		ptd016 protein. [refseq;acc:nm_016125]		Low confidence	30	5.26667	158	0
	Ranked	bcl2-related ovarian killer. [refseq;acc:nm_032515]	Subtracted	Low confidence	265.638	42.403	223.235	1
		cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Divided	High confidence	56.7841	1.32866	75.447	1
		ero1-like. [refseq;acc:nm_014584]	Subtracted		13853	6683	20536	0
		fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Divided		11543	1.69451	6812
			Subtracted	Low confidence	11543	4731	6812
		gbp protein isoform a. [refseq;acc:nm_017870]	Divided	Low confidence	305.399	1.23537	247.213	1
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Subtracted	High confidence	266.864	69.318	336.182	1
		leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	Divided	Low confidence	8082.33	1.53462	5266.67	0
	Squared	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Subtracted	High confidence	25050	17064.6	42114.6	0
		dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	Divided	High confidence	50.0828	8.80542	441	1
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Subtracted	Low confidence	122475	37292	159767
		necdin. [swissprot;acc:q99608]	Subtracted	High confidence	219048	89286	129762
		ptd016 protein. [refseq;acc:nm_016125]	Divided	Low confidence	0.213018	27.7377	5.90864	0
		putative dynein light chain protein dj8b22.1. [swissprot;acc:q9y3p0]	Subtracted	Low confidence	56144.4	9294.7	46849.7
		rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	Divided	High confidence	0.0766864	7668.64	0.00001
		vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	Divided	Low confidence	333506	1.4244	475045	1
	Rooted	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Subtracted	High confidence	203.673	21.035	182.638	1
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Subtracted	Low confidence	0	9.43398	9.43398	0
		hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Divided	High confidence	10.3085	8.45791	1.2188	0
		jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]	Subtracted	Low confidence	31.9296	15.8056	47.7352	1
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Subtracted	High confidence	12.4097	12.4097	0	0
		protein x 0004. [refseq;acc:nm_016301]	Divided	High confidence	51.6817	1.75117	29.5127	1
		ptd016 protein. [refseq;acc:nm_016125]		Low confidence	5.47723	2.29492	12.5698	0
		tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]		Low confidence	38.5678	1.27732	49.2633	1
18	Measured	60s ribosomal protein l37a. [swissprot;acc:p12751]		High confidence	305.45	11.6763	26.1599	0
		anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	Subtracted	High confidence	15411.3	1244.3	14167
		camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	Divided	Low confidence	99	5.21053	19
		cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Divided		5492.04	1.32027	7251	1
		homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Subtracted		15464.1	2108.6	17572.7
		microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Subtracted	High confidence	24255.7	6086.8	18168.9

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.

- http://analysis.yellowcouch.org/