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 2530 to 2579 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
317	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	Rooted	1	95.0526	85.3206	1.11406
	glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409]	Rooted	0	7.79521	7.32908	1.0636
	lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]	Squared		237.082	277.442	1.17024
	my016 protein. [sptrembl;acc:q9h3k6]	Measured		1770.21	1615.47	1.09579
	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232]	Squared	1	33982.3	43159.1	1.27005
	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	Ranked	0	19939	18778	1.06183
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Ranked	1	224.445	204.044	1.09998
318	glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189]	Rooted	0	7.80086	7.3344	1.0636
	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	Ranked	1	242.011	266.18	1.09987
	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388]	Squared		46739.9	59134.5	1.26518
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Rooted		95.0526	85.3206	1.11406
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured		34190.9	40795.8	1.19318
	protein cgi-147. [swissprot;acc:q9y3e5]	Measured	0	8396.12	9192.38	1.09484
	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	Squared		7372.32	6325.27	1.16553
	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]	Ranked		8918.54	9465.32	1.06131
319	60s ribosomal protein l19. [swissprot;acc:p14118]	Ranked	1	240.73	264.729	1.09969
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Measured	0	1388.45	1268.19	1.09483
	glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410]	Rooted	0	7.78379	7.31834	1.0636
	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855]	Squared	1	46739.9	59134.5	1.26518
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Measured		20911	24908.5	1.19117
	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	Rooted		49.0663	54.4978	1.1107
	scratch; scratch 1. [refseq;acc:nm_031309]	Squared	0	5976.46	5135.5	1.16375
	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]	Ranked	0	8918.54	9465.32	1.06131
320	40s ribosomal protein s29. [swissprot;acc:p30054]	Rooted	1	50.2784	45.294	1.11005
	adp-ribosylation factor 3. [swissprot;acc:p16587]	Ranked	0	11627.8	10958.2	1.0611
	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	Squared	0	5127.13	5964.46	1.16331
	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	Ranked	1	241.892	265.96	1.0995
	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099]	Squared	1	87971.9	69563.1	1.26463
	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	Rooted	0	28.7027	26.9929	1.06334
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Measured	1	20911	24908.5	1.19117
	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	Measured	0	142.802	156.3	1.09452
321	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	Ranked		11634.4	10989.9	1.05864
	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]	Squared		5671.94	6590.82	1.162
	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Ranked	1	241.892	265.959	1.09949
	dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513]	Measured	0	628.072	686.693	1.09333
	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]	Squared	1	33526	42390.2	1.2644
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Measured	1	20911	24908.5	1.19117
	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]	Rooted	0	42.9302	40.4104	1.06236
	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	Rooted	1	55.9231	62.0565	1.10968
322	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	Measured	0	1621.1	1771.04	1.09249
	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	Measured	1	20911	24908.5	1.19117
	casein kinase i alpha s-like. [refseq;acc:nm_145203]	Squared	0	7795.92	9052.52	1.16119
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Ranked	1	86.7483	78.8995	1.09948
	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]	Ranked	0	11634.4	10989.9	1.05864
	nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531]	Squared	1	33522.8	42384.8	1.26436
	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]	Rooted	0	46.9819	44.2892	1.0608
	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	Rooted	1	60.594	67.2244	1.10942
323	60s ribosomal protein l23a. [swissprot;acc:p29316]	Ranked		241.884	265.945	1.09947
	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	Rooted		50.3803	45.4193	1.10923
	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	Squared	0	5936.62	5112.71	1.16115

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/