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

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Showing element 823 to 872 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
103	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854]	Measured	0	197.333	290.667	1.47298
103	trophinin. [swissprot;acc:q12816]	Ranked	1	88.2482	110.265	1.24949
104	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Squared	1	407289	263351	1.54656
	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	Rooted	0	13.7413	17.8164	1.29656
	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	Ranked	1	252.371	202.016	1.24926
	jun dimerization protein. [refseq;acc:nm_130469]	Rooted	1	60.8365	77.7233	1.27758
	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	Squared	0	0.70501	1.50296	2.13183
	musashi 2 isoform a. [refseq;acc:nm_138962]	Measured	1	4241.57	5810.79	1.36996
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Measured	0	5106.93	7500.75	1.46874
	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765]	Ranked		9545	7868	1.21314
105	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	Ranked		17410.5	14360	1.21243
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Squared	1	407289	263351	1.54656
	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	Squared	0	2.36686	4.90793	2.0736
	fos-related antigen 2. [swissprot;acc:p15408]	Measured	0	3233.86	2208.1	1.46454
	fos-related antigen 2. [swissprot;acc:p15408]	Rooted	1	60.8675	77.7168	1.27682
	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448]	Rooted	0	25.8353	33.3747	1.29183
	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]	Ranked	1	266.716	333.165	1.24914
	musashi 1. [refseq;acc:nm_002442]	Measured		4241.57	5810.79	1.36996
106	cytohesin 4. [swissprot;acc:q9uia0]	Squared		407289	263351	1.54656
	elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897]	Ranked	0	16290.7	13464.8	1.20987
	nuclear protein ukp68. [refseq;acc:nm_024824]	Measured	1	4241.57	5810.79	1.36996
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Rooted	1	60.8692	77.7165	1.27678
	rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]	Squared	0	299.137	144.414	2.07139
	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	Measured		1251.66	858.525	1.45792
	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]	Rooted		5.47723	7.07107	1.29099
	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807]	Ranked	1	252.329	202.004	1.24913
107	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Measured		4266.04	5843.51	1.36977
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Squared		407289	263351	1.54656
	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	Rooted		60.875	77.7152	1.27664
	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	Ranked		252.309	201.998	1.24907
	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	Measured	0	326.677	472.605	1.4467
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	Rooted		22.2259	17.2182	1.29084
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Squared		4141.27	2000.69	2.06992
	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	Ranked		11853.5	9808.86	1.20845
108	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	Measured		292	421	1.44178
	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	Rooted		13.7191	17.6786	1.28861
	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]	Measured	1	4366.44	5899.76	1.35116
	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	Ranked		252.296	201.995	1.24902
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Squared		19321	12542.6	1.54043
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	Ranked	0	10585.3	12769.1	1.2063
	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	Squared	0	795.24	1645.86	2.06964
	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	Rooted	1	49.2925	62.397	1.26585
109	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	Measured	0	100	144	1.44
	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	Ranked	0	14466.8	12031.7	1.20239
	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	Ranked	1	266.933	333.281	1.24856
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Squared	1	19321	12542.6	1.54043
	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	Rooted	0	2.64575	3.38392	1.279
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Measured	1	4366.44	5899.76	1.35116
	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	Rooted	1	49.2923	62.3969	1.26585
	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	Squared	0	16.4056	33.4891	2.04132

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/