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

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Showing element 51 to 100 of 77072 in total

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Rank	green	Value Type	description	Network Comparison Type	network_comparison	Interaction Map	red
4	2.81207	Squared	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Divided	281207	High confidence	0.00001
	7.61577	Rooted	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Subtracted	21.6929	High confidence	29.3087
	9.43398		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Divided	943398	Low confidence	0.00001
	10.4403		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]		1044030	High confidence
	89	Measured	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		8900000	Low confidence
	89		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		8900000	High confidence
	4356		anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	Subtracted	2274	Low confidence	2082
	14977	Ranked	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Subtracted	9112		5865
	20617	Ranked	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	Divided	2.14604		9607
	21730	Measured	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Subtracted	3026	High confidence	18704
	21883	Ranked	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	2.45711		8906
	21888	Ranked	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Subtracted	10363		11525
	105900	Squared	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]		30453.3		75446.7
	295570	Squared	cytochrome c oxidase polypeptide viic, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p15954]		21739	Low confidence	273831
5	0	Rooted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		19.0788	High confidence	19.0788
	0.00001	Squared	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	Divided	32402.4	Low confidence	0.324024
	1.87479	Squared	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		187479	High confidence	0.00001
	7.68115	Rooted	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]		768115	Low confidence
	9.43398	Rooted	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		943398	High confidence
	17.5166	Measured	jumonji protein. [swissprot;acc:q92833]		1751660	Low confidence
	34.2643	Rooted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	18.1355	Low confidence	16.1288
	89	Measured	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Divided	8900000	High confidence	0.00001
	2740.13	Measured	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	2254.84	Low confidence	485.286
	11965.7	Ranked	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Divided	2.17144	High confidence	5510.5
	13216		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Subtracted	9070	Low confidence	22286
	19873		ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	Divided	1.82499	Low confidence	10889.4
	21888		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Subtracted	10363	High confidence	11525
	24446.3	Measured	histone h4. [swissprot;acc:p02304]		2673.2	High confidence	21773.1
	59791.4	Squared	ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08]		19680.5	Low confidence	40110.9
	105900	Squared	zinc finger protein 277. [swissprot;acc:q9nrm2]		30453.3	High confidence	75446.7
6	0	Rooted	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]		16.9115	Low confidence	16.9115
	0.00001	Measured	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Divided	1300000		13
		Squared	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]		32402.4		0.324024
		Rooted	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]		608276		6.08276
	1.87479	Squared	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		187479	High confidence	0.00001
	9.43398	Rooted			943398		0.00001
	27.8029	Rooted	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Subtracted	15.6374		12.1655
	89	Measured	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Divided	8900000		0.00001
	8836.85	Measured	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Subtracted	1244.48	Low confidence	7592.37
	9583.37	Ranked	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Divided	1.71877		5575.71
	13216		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Subtracted	9070		22286
	14977		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Subtracted	9112	High confidence	5865
	15339.2		ubiquitin protein ligase. [refseq;acc:nm_130466]	Divided	2.03897		7523
	15605.1	Measured	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Subtracted	2430.4		13174.7
	19295.9	Squared	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		19294.2	Low confidence	1.73869
	102814	Squared	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]		29733.2	High confidence	73080.8
7	0	Rooted	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]		16.9115	Low confidence	16.9115
	0.00001	Measured	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	Divided	231962		2.31962
	0.00001	Rooted	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]		608276		6.08276
	0.140962	Squared	jumonji protein. [swissprot;acc:q92833]		14096.2		0.00001

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/