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

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Showing element 551 to 600 of 77072 in total

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Network Comparison Type

: Divided

network_comparison	green	Value Type	red	Interaction Map	Rank	description
1	0.00001	Squared	0.00001	Low confidence	839	cobw-like protein. [refseq;acc:nm_018491]
					840	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
					841	gamma-glutamyltransferase. [sptrembl;acc:q14390]
					842	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
					843	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
		Rooted		High confidence	494	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
					495	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
					496	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
					497	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
					498	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
					499	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
					500	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
					501	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
					502	brca1 associated protein. [refseq;acc:nm_006768]
				Low confidence	837	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
					838	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
					839	cobw-like protein. [refseq;acc:nm_018491]
					840	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
					841	gamma-glutamyltransferase. [sptrembl;acc:q14390]
					842	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
					843	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
	394	Ranked	394	High confidence	500	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]
	394	Ranked	394	Low confidence	840
	17901.1	Squared	17901.1	High confidence	493	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]
	17901.1	Squared	17901.1	Low confidence	836
1.00005	1589.95	Measured	1589.87			myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]
1.00007	13844.1	Ranked	13845			protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]
1.00008	62.8986	Rooted	62.8936	High confidence	492	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]
1.00008	62.8986	Rooted	62.8936	High confidence	493	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]
1.0001	1573.69	Measured	1573.54	Low confidence	835	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]
1.00015	2710.41	Measured	2710.81	Low confidence	834	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975]
1.00017	6792.32	Squared	6791.15	High confidence	492	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]
1.0002	9357.07	Measured	9355.21	Low confidence	833	ganglioside induced differentiation associated protein 2; likely ortholog of mouse ganglioside-induced differentiation-associated-protein 2. [refseq;acc:nm_017686]
1.00023	27.1942	Rooted	27.188		836	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]
1.00032	11478.8	Ranked	11482.5		835	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]
1.00033	3507.42	Measured	3506.27		832	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]
1.00038	33.6926	Rooted	33.7054		835	ero1-like. [refseq;acc:nm_014584]
1.00041	42.6315	Rooted	42.6139	High confidence	491	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]
1.00041	16322.5	Ranked	16315.8	Low confidence	834	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]
1.00059	25.9014	Rooted	25.9167	Low confidence	834	putative forkhead box protein kiaa1041. [swissprot;acc:q9upw0]
1.00059	2411.78	Measured	2410.35	High confidence	493	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]
1.00065	1242.41	Measured	1243.22	Low confidence	831	hexokinase, type i (ec 2.7.1.1) (hk i) (brain form hexokinase). [swissprot;acc:p19367]
1.00068	28.7389	Rooted	28.7585		833	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]
1.00071	26139.1	Squared	26120.5		835	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]
1.00074	3462.18	Measured	3464.75		830	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]
1.00078	12904.6	Ranked	12894.5		833	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]
1.00082	28.7	Rooted	28.7235		832	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]
1.00085	22.2092	Rooted	22.228		831	transcription factor btf3 homolog 3. [swissprot;acc:q13892]
1.00086	1465.37	Measured	1464.11		829	alpha-nac protein. [sptrembl;acc:q9h009]
1.0009	3041.93	Squared	3044.68		834	scratch; scratch 1. [refseq;acc:nm_031309]

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/