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 12864 to 12913 of 77072 in total

Rank	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison
402	x-linked protein sts1769. [swissprot;acc:q99871]	Ranked	Divided	Low confidence	1	211.253	203.883	1.03615
403	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	Rooted	Subtracted		0	22.8712	24.621	1.7498
	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	Ranked	Divided		0	12779.3	11825.8	1.08063
	beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929]	Squared	Subtracted	High confidence	1	28190.4	33984.1	5793.7
	calcyphosine. [swissprot;acc:q13938]	Rooted		High confidence		59.5128	65.604	6.0912
	cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584]	Rooted		Low confidence		72.2945	75.765	3.4705
	eferin. [swissprot;acc:o75154]	Squared				34469.6	37645.4	3175.8
	elongation factor 1-beta (ef-1-beta). [swissprot;acc:p24534]	Rooted	Divided			70.3162	73.6827	1.04788
	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]	Measured	Divided	High confidence		5201.41	4479.76	1.16109
	glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410]	Squared	Subtracted	Low confidence	0	2454.14	2709.21	255.07
	glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840]	Squared	Divided	High confidence	1	39463.9	48362.1	1.22548
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Measured	Subtracted	Low confidence	0	864.333	746.529	117.804
		Rooted		High confidence		15.4896	14.7645	0.7251
	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	Ranked		Low confidence		10966.5	11580	613.5
	hepatocellularcarcinoma-associated antigen hca557a. [refseq;acc:nm_015433]	Measured	Divided	Low confidence		2800	2539	1.1028
	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	Squared	Divided	High confidence		1872.12	1754.91	1.06679
	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	Measured	Subtracted			2290.09	2264.37	25.72
	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	Ranked	Subtracted		1	228.468	246.338	17.87
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Measured	Divided		0	548.5	527.5	1.03981
	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	Measured	Subtracted	Low confidence	1	7398.26	7826.48	428.22
		Rooted	Divided	High confidence	1	59.6834	65.6741	1.10037
	pellino protein. [refseq;acc:nm_020651]	Squared		Low confidence	0	8120.06	9031.19	1.11221
	phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]	Ranked		High confidence	1	207.908	226.218	1.08807
	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	Rooted			0	19.4322	20.0671	1.03267
	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	Measured	Subtracted		1	6259.3	7190.91	931.61
	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	Ranked	Subtracted	Low confidence		200.049	192.942	7.107
	prolyl endopeptidase (ec 3.4.21.26) (post-proline cleaving enzyme) (pe). [swissprot;acc:p48147]	Squared	Divided	Low confidence		48608.6	45485.7	1.06866
	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]	Squared	Subtracted	High confidence	0	94.678	87.5656	7.1124
	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	Rooted	Divided	Low confidence		20.9858	22.7699	1.08501
	scribble. [refseq;acc:nm_015356]	Ranked	Subtracted	High confidence		12370.5	12719	348.5
	seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81]	Measured	Divided	Low confidence	1	8853.13	9319.56	1.05269
	three prime repair exonuclease 1 isoform c; deoxyribonuclease iii, dnaq/mutd (e. coli)-like; 3' repair exonuclease 1; atr interacting protein. [refseq;acc:nm_032166]	Ranked		Low confidence	1	211.253	203.883	1.03615
	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]	Ranked		High confidence	0	9783.63	10111.2	1.03348
404	40s ribosomal protein s3a. [swissprot;acc:p49241]	Rooted		High confidence		34.0198	32.9781	1.03159
	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]		Subtracted	Low confidence		22.9027	24.652	1.7493
	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]		Divided	Low confidence		20.9571	22.7303	1.08461
	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520]	Squared	Divided	High confidence	1	26819.1	32855.4	1.22507
	adiponectin receptor 2. [refseq;acc:nm_024551]	Measured	Subtracted	Low confidence		7170.39	7598.55	428.16
	alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733]	Squared	Subtracted	High confidence		28190.4	33984.1	5793.7
	atp synthase lipid-binding protein, mitochondrial precursor (ec 3.6.3.14) (atp synthase proteolipid p3) (atpase protein 9) (atpase subunit c). [swissprot;acc:p48201]	Squared	Divided	Low confidence		52108.1	48765.3	1.06855
	ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560]	Ranked	Divided	Low confidence	0	11658.5	12572.4	1.07839
	bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001]	Ranked	Subtracted	High confidence	1	228.463	246.33	17.867
	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	Rooted	Subtracted	High confidence	1	59.5128	65.604	6.0912
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Squared	Divided	Low confidence	0	28405.2	31588.7	1.11207
	dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5]	Rooted	Divided		1	72.2476	75.7022	1.04782
	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	Measured	Subtracted		0	1709.74	1591.99	117.75
	dna repair protein rad52 homolog. [swissprot;acc:p43351]	Ranked	Divided	High confidence	1	207.908	226.218	1.08807
	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	Squared	Subtracted	High confidence	0	3228.32	3221.55	6.77
	enigma protein; lim domain protein. [refseq;acc:nm_005451]	Ranked		Low confidence	0	13552.2	12940.6	611.6
	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060]	Measured		High confidence	1	7802.31	8731.82	929.51

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/