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

Results: HTML CSV LaTeX

Showing element 551 to 600 of 38536 in total

Network Comparison Type	Divided

Rank	Value Type	Filtered	description	Interaction Map	red	green	network_comparison	
35	Ranked	1	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [source:swissprot;acc:q13952]	High confidence	260.532	204.309	1.27519	
35	Ranked	1	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Low confidence	297.273	258.59	1.14959	
35	Squared	0	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [source:swissprot;acc:p12236]	High confidence	50.7031	647.816	12.7767	
35	Squared	0	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Low confidence	3.41692	0.355148	9.62112	
35	Squared	1	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	High confidence	106226	192141	1.80879	
35	Squared	1	necdin. [source:swissprot;acc:q99608]	Low confidence	82347.8	61881.5	1.33073	
35	Rooted	0	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [source:refseq;acc:nm_031938]	High confidence	23.8747	11.7898	2.02503	
35	Rooted	0	melanoma-associated antigen 2 (mage-2 antigen). [source:swissprot;acc:p43356]	Low confidence	9.84765	5.80678	1.69589	
35	Rooted	1	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	High confidence	40.2812	24.3679	1.65304	
35	Rooted	1	regulator of g-protein signaling 12 (rgs12). [source:swissprot;acc:o14924]	Low confidence	54.8296	63.2347	1.15329	
36	Measured	0	heparan sulfate 6-o-sulfotransferase 2. [source:refseq;acc:nm_147174]	High confidence	157	56	2.80357	
36	Measured	0	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Low confidence	105.5	35.5	2.97183	
36	Measured	1	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [source:swissprot;acc:p19086]	High confidence	1836.76	907.741	2.02344	
36	Measured	1	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [source:swissprot;acc:p01100]	Low confidence	6462.09	7593.77	1.17513	
36	Ranked	0	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). [source:swissprot;acc:q9byb4]	High confidence	22422	14964	1.4984	
36	Ranked	0	sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [source:swissprot;acc:q9nsi8]	Low confidence	13052.7	9520.8	1.37097	
36	Ranked	1	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [source:swissprot;acc:p23511]	High confidence	260.532	204.309	1.27519	
36	Ranked	1	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Low confidence	296.837	258.33	1.14906	
36	Squared	0	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [source:swissprot;acc:p49336]	High confidence	84.64	8.01325	10.5625	
36	Squared	0	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Low confidence	3.41692	0.355148	9.62112	
36	Squared	1	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	Low confidence	82347.8	61881.5	1.33073	
36	Squared	1	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	High confidence	106226	192141	1.80879	
36	Rooted	0	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [source:swissprot;acc:p80404]	High confidence	4.30525	2.18581	1.96964	
36	Rooted	0	hepatocellular carcinoma-associated protein hca1. [source:refseq;acc:nm_020932]	Low confidence	9.84765	5.80678	1.69589	
36	Rooted	1	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	Low confidence	55.7086	64.217	1.15273	
36	Rooted	1	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [source:swissprot;acc:p19086]	High confidence	40.2805	24.369	1.65294	
37	Measured	0	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	High confidence	334.401	934.348	2.79409	
37	Measured	0	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Low confidence	105.5	35.5	2.97183	
37	Measured	1	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [source:swissprot;acc:p11488]	High confidence	1836.76	907.763	2.02339	
37	Measured	1	jun dimerization protein. [source:refseq;acc:nm_130469]	Low confidence	6462.09	7593.77	1.17513	
37	Ranked	0	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [source:sptrembl;acc:q9uge0]	High confidence	3859	2582	1.49458	
37	Ranked	0	myotubularin related protein 8. [source:refseq;acc:nm_017677]	Low confidence	12302	8993.6	1.36786	
37	Ranked	1	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	Low confidence	250.244	217.843	1.14874	
37	Ranked	1	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	High confidence	322	253	1.27273	
37	Squared	0	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	High confidence	101.05	1034.13	10.2338	
37	Squared	0	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	Low confidence	3.41692	0.355148	9.62112	
37	Squared	1	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	Low confidence	82347.8	61881.5	1.33073	
37	Squared	1	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	High confidence	106226	192141	1.80879	
37	Rooted	0	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]	Low confidence	9.84765	5.80678	1.69589	
37	Rooted	0	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [source:swissprot;acc:p14678]	High confidence	4.83477	9.39626	1.94348	
37	Rooted	1	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [source:swissprot;acc:p11488]	High confidence	40.2805	24.3691	1.65293	
37	Rooted	1	testis-specific protein tex28. [source:swissprot;acc:o15482]	Low confidence	51.7058	59.166	1.14428	
38	Measured	0	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Low confidence	105.5	35.5	2.97183	
38	Measured	0	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [source:swissprot;acc:o43623]	High confidence	320.012	120.429	2.65727	
38	Measured	1	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [source:swissprot;acc:p19087]	High confidence	1836.76	907.774	2.02337	
38	Measured	1	rab11-family interacting protein 4. [source:refseq;acc:nm_032932]	Low confidence	7407.56	8696.7	1.17403	
38	Ranked	0	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [source:swissprot;acc:p49336]	High confidence	7230	10771	1.48976	
38	Ranked	0	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [source:swissprot;acc:q9np71]	Low confidence	6768.72	9243.55	1.36563	
38	Ranked	1	glucosamine-6-phosphate isomerase. [source:refseq;acc:nm_138335]	Low confidence	247.202	282.937	1.14456	
38	Ranked	1	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	High confidence	322	253	1.27273	

Legend:
- Rank is the rank after comparing the two networks
- 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/