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 3358 to 3407 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
420	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Rooted	0	6.9282	7.14143	1.03078
	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	Squared		2268.24	2378.75	1.04872
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Measured		18889	19496	1.03214
421	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]	Ranked		11186	10866.3	1.02942
	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Rooted	1	50.4666	45.9317	1.09873
	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681]	Squared	1	36933	44953.6	1.21717
	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	Squared	0	2892.28	2758.62	1.04845
	importin 4. [refseq;acc:nm_024658]	Measured		491.926	476.639	1.03207
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Rooted		6.9282	7.14143	1.03078
	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	Ranked	1	223.202	205.9	1.08403
	vav-2 protein. [swissprot;acc:p52735]	Measured		6660.02	7697.78	1.15582
422	60s ribosomal protein l5. [swissprot;acc:p46777]	Rooted		50.4641	45.9293	1.09873
	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	Squared	0	9431	9001.76	1.04768
	dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1]	Squared	1	25860	31475.4	1.21715
	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104]	Ranked	0	12581.7	12224.2	1.02925
	kappa b-ras 1. [refseq;acc:nm_020345]	Measured		1153.15	1117.36	1.03203
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Rooted		6.9282	7.14143	1.03078
	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	Measured	1	5206.9	6010.04	1.15425
	ras-related protein rab-37. [swissprot;acc:q96ax2]	Ranked	1	240.287	260.193	1.08284
423	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	Squared	0	8975.38	9403.03	1.04765
	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]	Ranked	0	5905	6073	1.02845
	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	Rooted	1	50.4663	45.9313	1.09873
	fibrillin 3. [refseq;acc:nm_032447]	Measured	0	14246	13809	1.03165
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	Rooted	0	6.9282	7.14143	1.03078
	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5]	Measured	1	5207.03	6010.1	1.15423
	ras-related protein rab-26. [swissprot;acc:q9ulw5]	Ranked		240.287	260.193	1.08284
	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	Squared		36735.7	44689.6	1.21652
424	60s ribosomal protein l23a. [swissprot;acc:p29316]	Rooted		50.4703	45.9373	1.09868
	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]	Ranked	0	9562.48	9298.93	1.02834
	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]	Ranked	1	240.287	260.193	1.08284
	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	Measured	0	3967.18	4091.59	1.03136
	mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713]	Squared	1	20259.5	24635.7	1.21601
	mstp028 protein. [refseq;acc:nm_031954]	Squared	0	105962	110835	1.04599
	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9]	Measured	1	5207.78	6010.45	1.15413
	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]	Rooted	0	48.9929	50.4997	1.03076
425	40s ribosomal protein s20. [swissprot;acc:p17075]	Rooted	1	50.0161	45.5318	1.09849
	max protein. [swissprot;acc:p25912]	Ranked		227.828	210.561	1.082
	mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439]	Squared		20258.6	24634.7	1.21601
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Measured	0	2070.81	2134.56	1.03079
	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	Measured	1	3729.02	4301.58	1.15354
	scribble. [refseq;acc:nm_015356]	Ranked	0	12370.5	12719	1.02817
	scribble. [refseq;acc:nm_015356]	Squared		4169.68	3987.55	1.04567
	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Rooted		133.419	129.687	1.02878
426	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	Squared		14907.5	15522.7	1.04127
	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]	Ranked		9412.67	9676.67	1.02805
	dynactin 4. [refseq;acc:nm_032486]	Ranked	1	233.142	252.253	1.08197
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Rooted	0	22.1458	22.7768	1.02849
	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	Rooted	1	55.1073	60.5285	1.09838
	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]	Measured	1	5942.49	6853.15	1.15325
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Measured	0	2071.59	2133.83	1.03004

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/