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

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Showing element 551 to 600 of 38536 in total

Network Comparison Type

: Divided

Rank	Value Type	description	Filtered	Interaction Map	red	green	network_comparison
35	Ranked	protein tyrosine phosphatase type iva, member 2 isoform 1; protein tyrosine phosphatase iva2; protein tyrosine phosphatase iva; phosphatase of regenerating liver 2. [refseq;acc:nm_003479]	0	Low confidence	11808.5	16243	1.37553
	Ranked	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	1	Low confidence	297.273	258.59	1.14959
	Squared	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	1	High confidence	106226	192141	1.80879
		adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	0	High confidence	50.7031	647.816	12.7767
		melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	0	Low confidence	3.41692	0.355148	9.62112
		necdin. [swissprot;acc:q99608]	1	Low confidence	82347.8	61881.5	1.33073
	Rooted	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	0	High confidence	23.8747	11.7898	2.02503
		guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	1	High confidence	40.2812	24.3679	1.65304
		melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	0	Low confidence	9.84765	5.80678	1.69589
		regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924]	1	Low confidence	54.8296	63.2347	1.15329
36	Measured	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	1	High confidence	1836.76	907.741	2.02344
		heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	0	High confidence	157	56	2.80357
		melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	0	Low confidence	105.5	35.5	2.97183
		proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	1	Low confidence	6462.09	7593.77	1.17513
	Ranked	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	1	High confidence	260.532	204.309	1.27519
		guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	0	High confidence	22422	14964	1.4984
		sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8]	0	Low confidence	13052.7	9520.8	1.37097
		tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	1	Low confidence	296.837	258.33	1.14906
	Squared	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	0	High confidence	84.64	8.01325	10.5625
		melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	0	Low confidence	3.41692	0.355148	9.62112
		melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	1	Low confidence	82347.8	61881.5	1.33073
		pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	1	High confidence	106226	192141	1.80879
	Rooted	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]	0	High confidence	4.30525	2.18581	1.96964
		chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	1	Low confidence	55.7086	64.217	1.15273
		guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	1	High confidence	40.2805	24.369	1.65294
		hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	0	Low confidence	9.84765	5.80678	1.69589
37	Measured	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	0	High confidence	334.401	934.348	2.79409
		guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	1	High confidence	1836.76	907.763	2.02339
		jun dimerization protein. [refseq;acc:nm_130469]	1	Low confidence	6462.09	7593.77	1.17513
		melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	0		105.5	35.5	2.97183
	Ranked	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	1		250.244	217.843	1.14874
		dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	0	High confidence	3859	2582	1.49458
		myotubularin related protein 8. [refseq;acc:nm_017677]	0	Low confidence	12302	8993.6	1.36786
		protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	1	High confidence	322	253	1.27273
	Squared	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	0	High confidence	101.05	1034.13	10.2338
		melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	0	Low confidence	3.41692	0.355148	9.62112
		melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	1	Low confidence	82347.8	61881.5	1.33073
		pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]		High confidence	106226	192141	1.80879
	Rooted	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]		High confidence	40.2805	24.3691	1.65293
		melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	0	Low confidence	9.84765	5.80678	1.69589
		small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	0	High confidence	4.83477	9.39626	1.94348
		testis-specific protein tex28. [swissprot;acc:o15482]	1	Low confidence	51.7058	59.166	1.14428
38	Measured	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	1	High confidence	1836.76	907.774	2.02337
		melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	0	Low confidence	105.5	35.5	2.97183
		rab11-family interacting protein 4. [refseq;acc:nm_032932]	1	Low confidence	7407.56	8696.7	1.17403
		zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	0	High confidence	320.012	120.429	2.65727
	Ranked	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	0	High confidence	7230	10771	1.48976
		glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335]	1	Low confidence	247.202	282.937	1.14456
		microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	1	High confidence	322	253	1.27273
		williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]	0	Low confidence	6768.72	9243.55	1.36563

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/