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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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 [...,...].

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

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Showing element 51 to 100 of 77072 in total

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Network Comparison Type

: Subtracted

network_comparison	green	Value Type	red	Interaction Map	Rank	description
0	0	Rooted	0	Low confidence	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		17901.1	Low confidence	836
0.00219609	0		0.00219609	Low confidence	835	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]
0.005	62.8986	Rooted	62.8936	High confidence	492	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]
0.005	62.8986		62.8936	High confidence	493	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]
0.0062	27.1942		27.188	Low confidence	836	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]
0.0128	33.6926		33.7054		835	ero1-like. [refseq;acc:nm_014584]
0.0153	25.9014		25.9167		834	putative forkhead box protein kiaa1041. [swissprot;acc:q9upw0]
0.0176	42.6315		42.6139	High confidence	491	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]
0.0188	22.2092		22.228	Low confidence	833	transcription factor btf3 homolog 3. [swissprot;acc:q13892]
0.0196	28.7389		28.7585	Low confidence	832	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]
0.023	24.4079		24.4309	High confidence	490	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]
0.0235	28.7		28.7235	Low confidence	831	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]
0.0287	25.883		25.9117	Low confidence	830	forkhead box protein j1 (forkhead-related protein fkhl13) (hepatocyte nuclear factor 3 forkhead homolog 4) (hfh-4). [swissprot;acc:q92949]
0.0294	22.9676		22.997	High confidence	489	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210]
0.0349	27.3392		27.3043	Low confidence	829	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]
0.0355	28.6975		28.733	Low confidence	828	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]
0.037239	0.145878	Squared	0.108639	High confidence	492	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]
0.0385	20.9563	Rooted	20.9948	Low confidence	827	dead-box protein. [refseq;acc:nm_018665]
0.0397632	0.0854438	Squared	0.125207	High confidence	491	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]
0.0397632	0.0854438	Squared	0.125207	Low confidence	834
0.0399	12.4629	Rooted	12.5028	High confidence	488	pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790]
0.04	0	Squared	0.04	Low confidence	833	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
0.041	22.8963	Rooted	22.8553		826	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]
0.0423	28.8142	Rooted	28.7719		825	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]
0.046153	0.227456	Squared	0.273609		832	adapter-related protein complex 2 alpha 1 subunit (alpha-adaptin a) (adaptor protein complex ap-2 alpha-1 subunit) (clathrin assembly protein complex 2 alpha-a large chain) (100 kda coated vesicle protein a) (plasma membrane adaptor ha2/ap2 adaptin alpha a subunit). [swissprot;acc:o95782]
0.0478	26.3602	Rooted	26.3124		824	my016 protein. [sptrembl;acc:q9h3k6]
0.0511	25.3889		25.44	High confidence	487	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]
0.0521	25.8508		25.9029	Low confidence	823	forkhead box protein f1 (forkhead-related protein fkhl5) (forkhead- related transcription factor 1) (freac-1) (forkhead-related activator- 1). [swissprot;acc:q12946]
0.05248	6.30196		6.24948	High confidence	486	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]
0.0530177	0.0532544	Squared	0.000236686	High confidence	490	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]
0.0534	31.685	Rooted	31.7384	Low confidence	822	histone h1.4 (histone h1b). [swissprot;acc:p10412]
0.0554	18.4766	Rooted	18.532		821	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]
0.058935	0.378698	Squared	0.437633		831	probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1]
0.0609467	0.0318343		0.092781	High confidence	489	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]
0.0609467	0.0318343		0.092781	Low confidence	830
0.0615	26.7508	Rooted	26.6893		820	40s ribosomal protein s26. [swissprot;acc:p02383]
0.0622	25.8368		25.899		819	forkhead box protein d4 (forkhead-related protein fkhl9) (forkhead- related transcription factor 5) (freac-5) (myeloid factor-alpha). [swissprot;acc:q12950]
0.0639	21.5864		21.5225		818	tubulin beta-5 chain (tubulin 5 beta). [swissprot;acc:p04350]
0.0643	25.834		25.8983		817	forkhead box protein d4b (myeloid factor-gamma). [swissprot;acc:q8wxt5]
0.0653	25.8326		25.8979		816	forkhead box protein d4-like 1. [swissprot;acc:q9nu39]
0.069	30.6032		30.6722		815	limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]

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/