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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1850 to 1899 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
232	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Measured	0	1663.73	1906.28	1.14579
	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	Measured	1	9035	7279.6	1.24114
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Rooted	0	15.6205	13.9284	1.12149
	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	Ranked	0	12394.7	11240.2	1.10271
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Rooted	1	137.446	120.823	1.13758
	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1]	Squared		42411.6	55802.1	1.31573
	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	Ranked		239.336	267.879	1.11926
233	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	Ranked	0	9586.97	10560	1.1015
	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]	Squared		5294.83	3966.41	1.33492
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Rooted		22.1446	19.7536	1.12104
	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	Ranked	1	239.32	267.842	1.11918
	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	Measured	0	348.823	399.534	1.14538
	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]	Squared	1	42411.6	55802.1	1.31573
	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Rooted		137.446	120.823	1.13758
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Measured		9035	7279.6	1.24114
234	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	Ranked		287.41	256.835	1.11905
	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	Rooted	0	16.0012	17.8885	1.11795
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Rooted	1	137.446	120.823	1.13758
	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829]	Squared	0	5294.83	3966.41	1.33492
	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]	Squared	1	42411.6	55802.1	1.31573
	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	Measured	1	5181.2	6410.58	1.23728
	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	Ranked	0	16614	18296	1.10124
	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	Measured		5202.89	4550.64	1.14333
235	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	Ranked		14554.5	16027.9	1.10123
	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]	Measured		1612.86	1843.92	1.14326
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Rooted	1	137.446	120.823	1.13758
	nitrogen fixation cluster-like. [refseq;acc:nm_014301]	Squared		42411.6	55802.1	1.31573
	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	Ranked		227.357	254.15	1.11785
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Measured		5181.2	6410.58	1.23728
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Squared	0	23310.5	31089.6	1.33372
	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	Rooted	0	26.1597	29.2445	1.11792
236	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Rooted	1	137.446	120.823	1.13758
	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753]	Measured	0	2715.75	3103.01	1.1426
	pnas-18. [sptrembl;acc:q9bzu3]	Rooted		24.2086	21.6857	1.11634
	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	Squared		18175.2	13699.8	1.32668
	pp3111 protein. [refseq;acc:nm_022156]	Ranked	1	227.357	254.15	1.11785
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Ranked	0	15245.4	16788.5	1.10122
	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	Measured	1	4723.53	5828.46	1.23392
	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8]	Squared	1	42411.6	55802.1	1.31573
237	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	Squared	0	5219.15	3979.89	1.31138
	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	Ranked		9984	9067	1.10114
	dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]	Rooted		21.2911	23.7622	1.11606
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Rooted	1	137.446	120.823	1.13758
	p28 ing5. [refseq;acc:nm_032329]	Measured	0	2551.23	2243.69	1.13707
	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502]	Squared	1	42411.6	55802.1	1.31573
	syntaxin 18. [swissprot;acc:q9p2w9]	Ranked		227.357	254.15	1.11785
	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	Measured		4567.04	5631.2	1.23301
238	casein kinase i alpha s-like. [refseq;acc:nm_145203]	Measured	0	2198.47	1933.94	1.13678
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Ranked		12677.7	13941.7	1.0997
	lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]	Rooted		20.6514	18.5098	1.1157

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/