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

Results: HTML CSV LaTeX

Showing element 1501 to 1550 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
188	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Measured	1	4571.89	5864.86	1.28281
	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]	Rooted	1	46.0352	53.0192	1.15171
	transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675]	Squared	0	157.095	228.024	1.4515
	udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]	Rooted	0	32.4121	28.377	1.1422
189	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	Squared	1	41502.9	30836.8	1.34589
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Squared	0	232467	160184	1.45125
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Measured	1	4571.89	5864.86	1.28281
	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	Ranked	1	226.582	198.444	1.14179
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	Measured	0	1249.24	1023.76	1.22025
	sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4]	Ranked	0	10634.4	9465	1.12355
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Rooted	1	46.0352	53.0192	1.15171
	udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133]	Rooted	0	32.4121	28.377	1.1422
190	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087]	Squared	1	71389.9	96037.6	1.34525
	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]	Measured		4571.89	5864.86	1.28281
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Rooted		149.165	129.699	1.15009
	glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075]	Rooted	0	32.4121	28.377	1.1422
	high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]	Ranked		18809.5	16764.2	1.122
	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	Measured		14	11.5	1.21739
	transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525]	Squared		158.413	229.842	1.4509
	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	Ranked	1	226.582	198.444	1.14179
191	aquaporin 5. [swissprot;acc:p55064]	Squared	1	71388.5	96035.2	1.34525
	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	Measured	0	743.066	904.149	1.21678
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Ranked	1	226.582	198.444	1.14179
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Rooted	1	63.1192	72.584	1.14995
	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]	Ranked	0	18809.5	16764.2	1.122
	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	Measured	1	4638.1	5923.4	1.27712
	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]	Squared	0	40674.4	28034.4	1.45087
	udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537]	Rooted	0	32.4121	28.377	1.1422
192	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	Measured	1	17757.5	14008	1.26767
	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	Squared	1	71387.4	96033.4	1.34524
	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	Squared	0	3480.56	5039.04	1.44777
	musashi 2 isoform a. [refseq;acc:nm_138962]	Ranked	1	227.491	199.458	1.14055
	sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4]	Measured	0	1965.47	2389.69	1.21584
	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	Rooted	1	53.6107	61.5862	1.14877
	t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227]	Ranked	0	12715.9	11333.2	1.122
	udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855]	Rooted		32.4121	28.377	1.1422
193	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	Squared		3338.97	4832.12	1.44719
	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	Squared	1	71386.9	96032.5	1.34524
	musashi 1. [refseq;acc:nm_002442]	Ranked		227.491	199.458	1.14055
	nostrin. [refseq;acc:nm_052946]	Rooted		59.6399	51.9242	1.1486
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured	0	23818.1	19621.3	1.21389
	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]	Rooted	0	29.5635	33.7491	1.14158
	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	Measured	1	17756.5	14007.3	1.26766
	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	Ranked	0	10899.5	12217.4	1.12091
194	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972]	Squared	1	71346.6	95965.1	1.34505
	cyclin g2. [swissprot;acc:q16589]	Measured		17738.6	13995.7	1.26743
	eap30 subunit of ell complex. [refseq;acc:nm_007241]	Rooted		59.6399	51.9242	1.1486
	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388]	Squared	0	668.421	962.098	1.43936
	kappa b-ras 1. [refseq;acc:nm_020345]	Ranked		12657.7	11299.1	1.12024
	keratin associated protein 9.2. [refseq;acc:nm_031961]	Rooted		23.871	20.9159	1.14128

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/