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.

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 Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 501 to 550 of 33156 in total

Network Comparison Type	Divided
Filtered	1

Rank	description	Value Type	Interaction Map	red	green	network_comparison	
63	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	Squared	High confidence	219048	129762	1.68808	
63	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	Measured	High confidence	4489.19	2765.82	1.6231	
63	putative rna-binding protein 7 (rna binding motif protein 7). [source:swissprot;acc:q9y580]	Ranked	Low confidence	265.688	239.902	1.10749	
63	t-box transcription factor tbx19 (t-box protein 19). [source:swissprot;acc:o60806]	Rooted	Low confidence	61.4851	68.1264	1.10801	
64	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Rooted	High confidence	63.8686	47.2654	1.35128	
64	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	Measured	High confidence	4489.19	2765.82	1.6231	
64	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [source:swissprot;acc:p50152]	Ranked	High confidence	266.868	336.159	1.25965	
64	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	Squared	High confidence	219048	129762	1.68808	
64	neurochondrin. [source:refseq;acc:nm_014284]	Squared	Low confidence	73677.6	57498.7	1.28138	
64	rab11-family interacting protein 4. [source:refseq;acc:nm_032932]	Rooted	Low confidence	73.6221	81.4944	1.10693	
64	retinal short-chain dehydrogenase/reductase 3. [source:refseq;acc:nm_016246]	Measured	Low confidence	15464.1	17572.7	1.13635	
64	transcription factor jun-d. [source:swissprot;acc:p17535]	Ranked	Low confidence	202.709	183.361	1.10552	
65	eferin. [source:swissprot;acc:o75154]	Rooted	Low confidence	73.6221	81.4944	1.10693	
65	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Rooted	High confidence	63.8686	47.2654	1.35128	
65	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	Ranked	High confidence	267.136	336.077	1.25807	
65	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	Squared	High confidence	219048	129762	1.68808	
65	neuralized-like. [source:refseq;acc:nm_004210]	Measured	High confidence	1657.68	2690.25	1.6229	
65	septin 6. [source:swissprot;acc:q14141]	Measured	Low confidence	13005.8	14773.7	1.13593	
65	septin-like protein kiaa0202 (fragment). [source:swissprot;acc:q92599]	Squared	Low confidence	75490.8	95493.3	1.26497	
65	transcription factor jun-b. [source:swissprot;acc:p17275]	Ranked	Low confidence	202.728	183.388	1.10546	
66	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Rooted	Low confidence	55.8923	61.8016	1.10573	
66	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Rooted	High confidence	63.8686	47.2654	1.35128	
66	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [source:swissprot;acc:p29992]	Ranked	High confidence	267.136	336.077	1.25807	
66	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Squared	High confidence	219048	129762	1.68808	
66	mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [source:refseq;acc:nm_020749]	Ranked	Low confidence	221.902	200.783	1.10518	
66	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [source:swissprot;acc:q9ui09]	Measured	High confidence	1991.03	3221.38	1.61795	
66	septin 10 isoform 1. [source:refseq;acc:nm_144710]	Squared	Low confidence	74803.9	94281	1.26038	
66	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [source:swissprot;acc:p18583]	Measured	Low confidence	4900.7	5555.81	1.13368	
67	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Measured	High confidence	6475.5	10307.5	1.59177	
67	brachyury protein (t protein). [source:swissprot;acc:o15178]	Rooted	Low confidence	61.687	68.2003	1.10559	
67	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [source:swissprot;acc:p19087]	Ranked	High confidence	267.14	336.075	1.25805	
67	hira-interacting protein 5 (cgi-33). [source:swissprot;acc:q9ums0]	Measured	Low confidence	12176.9	13781.8	1.1318	
67	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Squared	High confidence	219048	129762	1.68808	
67	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	Rooted	High confidence	63.8686	47.2654	1.35128	
67	retinoblastoma-associated factor 600. [source:refseq;acc:nm_020765]	Ranked	Low confidence	165.535	149.799	1.10505	
67	septin 6. [source:swissprot;acc:q14141]	Squared	Low confidence	74378.4	93531.9	1.25751	
68	60s ribosomal protein l37a. [source:swissprot;acc:p12751]	Ranked	Low confidence	239.692	217.005	1.10455	
68	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Measured	High confidence	6475.5	10307.5	1.59177	
68	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	Rooted	High confidence	63.8686	47.2654	1.35128	
68	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [source:swissprot;acc:p19086]	Ranked	High confidence	267.139	336.075	1.25805	
68	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Squared	High confidence	219048	129762	1.68808	
68	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Measured	Low confidence	19498.1	17265.4	1.12932	
68	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	Rooted	Low confidence	55.9786	61.8641	1.10514	
68	retinoblastoma-associated factor 600. [source:refseq;acc:nm_020765]	Squared	Low confidence	27909.1	35068.7	1.25653	
69	amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [source:refseq;acc:nm_138817]	Measured	Low confidence	6991.78	7848.45	1.12253	
69	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [source:swissprot;acc:q02410]	Rooted	Low confidence	60.7884	67.1136	1.10405	
69	delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (ec 1.5.1.12) (p5c dehydrogenase). [source:swissprot;acc:p30038]	Squared	Low confidence	80538.1	64191.7	1.25465	
69	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [source:swissprot;acc:p11488]	Ranked	High confidence	267.14	336.075	1.25805	
69	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	Squared	High confidence	219048	129762	1.68808	
69	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	Rooted	High confidence	27.9136	37.2872	1.33581	

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/