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

Results: HTML CSV LaTeX

Showing element 1475 to 1524 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	Value Type	description	Filtered	red	green	network_comparison
185	Ranked	adiponectin receptor 2. [refseq;acc:nm_024551]	1	281.582	246.371	1.14292
	Ranked	zinc finger protein 277. [swissprot;acc:q9nrm2]	0	6279.56	5569.42	1.12751
	Squared	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	0	0.125207	0.0854438	1.46537
	Squared	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	1	41502.9	30836.8	1.34589
	Rooted	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	0	30.6682	26.8335	1.14291
	Rooted	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	1	153.578	133.176	1.1532
186	Measured	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	1	4071.1	5251.75	1.29001
	Measured	glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311]	0	470.251	384.733	1.22228
	Ranked	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	0	11935.1	10592.8	1.12672
	Ranked	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]	1	226.582	198.444	1.14179
	Squared	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]	1	41502.9	30836.8	1.34589
	Squared	huntingtin interacting protein c. [refseq;acc:nm_012272]	0	5086.87	3492.66	1.45645
	Rooted	60s ribosomal protein l15. [swissprot;acc:p39030]	0	19.482	17.0546	1.14233
	Rooted	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	1	153.578	133.176	1.1532
187	Measured	importin 9. [refseq;acc:nm_018085]	0	1143.55	1397.66	1.22221
	Measured	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	1	4569.48	5885.79	1.28807
	Ranked	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	0	9955.22	11213.7	1.12641
	Ranked	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	1	226.582	198.444	1.14179
	Squared	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]	1	41502.9	30836.8	1.34589
	Squared	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]	0	8660.1	5963.73	1.45213
	Rooted	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	1	153.548	133.153	1.15317
	Rooted	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]	0	32.4121	28.377	1.1422
188	Measured	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	0	1143.55	1397.66	1.22221
	Measured	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	1	4571.89	5864.86	1.28281
	Ranked	60s ribosomal protein l15. [swissprot;acc:p39030]	0	11745.2	13203.1	1.12413
	Ranked	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	1	226.582	198.444	1.14179
	Squared	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]	1	41502.9	30836.8	1.34589
	Squared	transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675]	0	157.095	228.024	1.4515
	Rooted	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	1	46.0352	53.0192	1.15171
	Rooted	udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]	0	32.4121	28.377	1.1422
189	Measured	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	1	4571.89	5864.86	1.28281
	Measured	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	0	1249.24	1023.76	1.22025
	Ranked	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	1	226.582	198.444	1.14179
	Ranked	sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4]	0	10634.4	9465	1.12355
	Squared	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	1	41502.9	30836.8	1.34589
	Squared	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	0	232467	160184	1.45125
	Rooted	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	1	46.0352	53.0192	1.15171
	Rooted	udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133]	0	32.4121	28.377	1.1422
190	Measured	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]	1	4571.89	5864.86	1.28281
	Measured	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	0	14	11.5	1.21739
	Ranked	high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]	0	18809.5	16764.2	1.122
	Ranked	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	1	226.582	198.444	1.14179
	Squared	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087]	1	71389.9	96037.6	1.34525
	Squared	transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525]	0	158.413	229.842	1.4509
	Rooted	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	1	149.165	129.699	1.15009
	Rooted	glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075]	0	32.4121	28.377	1.1422
191	Measured	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	0	743.066	904.149	1.21678
	Measured	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	1	4638.1	5923.4	1.27712
	Ranked	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	1	226.582	198.444	1.14179
	Ranked	sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]	0	18809.5	16764.2	1.122

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/