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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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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 301 to 350 of 77072 in total

Filtered

: 0
Value Type

: Squared

green	network_comparison	Interaction Map	red	Network Comparison Type	Rank	description
0.615621	0.070296	High confidence	0.545325	Subtracted	472	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]
					473	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
					474	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]
					475	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
					476	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
					477	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
					478	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
					479	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
					480	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
					481	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
					482	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
					483	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
					484	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
					485	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
					486	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
					487	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
					488	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]
	1.12891			Divided	348	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]
					349	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
					350	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]
					351	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
					352	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
					353	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
					354	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
					355	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
					356	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
					357	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
					358	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
					359	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
					360	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
					361	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
					362	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
					363	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
					364	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]
0.664852	0.374911	Low confidence	0.289941	Subtracted	819	acidic leucine-rich nuclear phosphoprotein 32 family member c (tumorigenic protein pp32r1). [swissprot;acc:o43423]
	0.374911			Subtracted	820	acidic leucine-rich nuclear phosphoprotein 32 family member d (tumorigenic protein pp32r2). [swissprot;acc:o95626]
	2.29306			Divided	94	acidic leucine-rich nuclear phosphoprotein 32 family member c (tumorigenic protein pp32r1). [swissprot;acc:o43423]
	2.29306			Divided	95	acidic leucine-rich nuclear phosphoprotein 32 family member d (tumorigenic protein pp32r2). [swissprot;acc:o95626]
0.697197	0.653614	High confidence	0.0435834	Subtracted	454	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]
	0.653614	Low confidence		Subtracted	812
	15.9968	High confidence		Divided	34
	15.9968	Low confidence		Divided	22
0.742249	0.324734	High confidence	0.417515	Subtracted	462	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]
					463	serpin b11. [swissprot;acc:q96p15]
					464	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
		Low confidence			823	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]
					824	serpin b11. [swissprot;acc:q96p15]
					825	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
	1.77778	High confidence		Divided	137	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]
	1.77778	High confidence		Divided	138	serpin b11. [swissprot;acc:q96p15]

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/