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

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Showing element 551 to 600 of 29840 in total

Interaction Map

: High confidence

Rank	Value Type	description	Filtered	red	Network Comparison Type	green	network_comparison
35	Ranked	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	0	3208.8	Divided	4871.6	1.5182
	Ranked	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	1	260.532		204.309	1.27519
	Squared	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	1	106226		192141	1.80879
		adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	0	50.7031		647.816	12.7767
		bystin. [swissprot;acc:q13895]	0	26569.7	Subtracted	32857.7	6288
		mitochondrial solute carrier protein. [refseq;acc:nm_145305]	1	106226		192141	85915
	Rooted	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	1	140.508		122.878	17.63
		beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	0	23.8747	Divided	11.7898	2.02503
		guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	1	40.2812	Divided	24.3679	1.65304
		serpin b12. [swissprot;acc:q96p63]	0	10.2928	Subtracted	1.18697	9.10583
36	Measured	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	1	1836.76	Divided	907.741	2.02344
		heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	0	157	Divided	56	2.80357
		melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	1	23693.7	Subtracted	18263	5430.7
		oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	0	1586.07	Subtracted	925.298	660.772
	Ranked	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	1	260.532	Divided	204.309	1.27519
		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]	0	22422	Divided	14964	1.4984
		nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	0	13292.2	Subtracted	8691.76	4600.44
		protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	1	320.927	Subtracted	254.434	66.493
	Squared	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	0	84.64	Divided	8.01325	10.5625
		cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	1	227160	Subtracted	146079	81081
		huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	0	363053	Subtracted	369010	5957
		pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	1	106226	Divided	192141	1.80879
	Rooted	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	4.30525		2.18581	1.96964
		guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	1	40.2805		24.369	1.65294
		hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	0	10.3085	Subtracted	1.2188	9.0897
		protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	1	26.0288	Subtracted	43.1914	17.1626
37	Measured	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	0	334.401	Divided	934.348	2.79409
		guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	1	1836.76	Divided	907.763	2.02339
		melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	1	23693.7	Subtracted	18263	5430.7
		wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	0	5202.89	Subtracted	4550.64	652.25
	Ranked	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]		3859	Divided	2582	1.49458
		dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]		12128.3	Subtracted	7533.33	4594.97
		guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]	1	266.716	Subtracted	333.165	66.449
		protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	1	322	Divided	253	1.27273
	Squared	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	0	101.05	Divided	1034.13	10.2338
		dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	0	32413.7	Subtracted	38271.3	5857.6
		pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	1	106226	Divided	192141	1.80879
		trs85 homolog. [swissprot;acc:q9y2l5]		227160	Subtracted	146079	81081
	Rooted	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]		40.2805	Divided	24.3691	1.65293
		microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]		26.0288	Subtracted	43.1914	17.1626
		nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	0	16.3095	Subtracted	25.3969	9.0874
		small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]		4.83477	Divided	9.39626	1.94348
38	Measured	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]		5497.01	Subtracted	6127.24	630.23
		guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	1	1836.76	Divided	907.774	2.02337
		melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	1	23693.7	Subtracted	18263	5430.7
		zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	0	320.012	Divided	120.429	2.65727
	Ranked	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	0	7230	Divided	10771	1.48976
		guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	1	266.933	Subtracted	333.281	66.348
		microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	1	322	Divided	253	1.27273
		p28 ing5. [refseq;acc:nm_032329]	0	12124.8	Subtracted	7562.05	4562.75

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/