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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 551 to 600 of 29840 in total

Interaction Map

: High confidence

Rank	Network Comparison Type	Value Type	description	green	red	Filtered	network_comparison
35	Divided	Rooted	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	11.7898	23.8747	0	2.02503
	Divided	Rooted	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	24.3679	40.2812	1	1.65304
	Subtracted	Measured	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	898	1603	0	705
		Measured	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	18263	23693.7	1	5430.7
		Ranked	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]	335.359	267.636	1	67.723
		Ranked	importin 9. [refseq;acc:nm_018085]	8691.76	13292.2	0	4600.44
		Squared	bystin. [swissprot;acc:q13895]	32857.7	26569.7	0	6288
		Squared	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	192141	106226	1	85915
		Rooted	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	122.878	140.508	1	17.63
		Rooted	serpin b12. [swissprot;acc:q96p63]	1.18697	10.2928	0	9.10583
36	Divided	Measured	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	907.741	1836.76	1	2.02344
		Measured	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	56	157	0	2.80357
		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]	204.309	260.532	1	1.27519
		Ranked	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]	14964	22422	0	1.4984
		Squared	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	8.01325	84.64	0	10.5625
		Squared	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	192141	106226	1	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]	2.18581	4.30525	0	1.96964
		Rooted	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	24.369	40.2805	1	1.65294
	Subtracted	Measured	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	18263	23693.7	1	5430.7
		Measured	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	925.298	1586.07	0	660.772
		Ranked	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	8691.76	13292.2	0	4600.44
		Ranked	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	254.434	320.927	1	66.493
		Squared	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]	146079	227160	1	81081
		Squared	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	369010	363053	0	5957
		Rooted	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	1.2188	10.3085	0	9.0897
		Rooted	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	43.1914	26.0288	1	17.1626
37	Divided	Measured	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	934.348	334.401	0	2.79409
		Measured	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	907.763	1836.76	1	2.02339
		Ranked	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	2582	3859	0	1.49458
		Ranked	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	253	322	1	1.27273
		Squared	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	1034.13	101.05	0	10.2338
		Squared	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	192141	106226	1	1.80879
		Rooted	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	24.3691	40.2805	1	1.65293
		Rooted	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	9.39626	4.83477	0	1.94348
	Subtracted	Measured	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	18263	23693.7	1	5430.7
		Measured	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	4550.64	5202.89	0	652.25
		Ranked	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	7533.33	12128.3	0	4594.97
		Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]	333.165	266.716	1	66.449
		Squared	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	38271.3	32413.7	0	5857.6
		Squared	trs85 homolog. [swissprot;acc:q9y2l5]	146079	227160	1	81081
		Rooted	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	43.1914	26.0288	1	17.1626
		Rooted	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]	25.3969	16.3095	0	9.0874
38	Divided	Measured	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	907.774	1836.76	1	2.02337
		Measured	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	120.429	320.012	0	2.65727
		Ranked	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	10771	7230	0	1.48976
		Ranked	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	253	322	1	1.27273
		Squared	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	0.52284	4.84	0	9.25713
		Squared	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	192141	106226	1	1.80879
		Rooted	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	24.3692	40.2804	1	1.65292
		Rooted	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	6.97663	3.62029	0	1.92709

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/