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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 38536 in total

Filtered

: 0
Value Type

: Measured
Network Comparison Type

: Divided

green	description	network_comparison	Interaction Map	red	Rank
29	abl-philin 2. [refseq;acc:nm_032327]	1.65517	Low confidence	48	83
31	adapter-related protein complex 2 alpha 1 subunit (alpha-adaptin a) (adaptor protein complex ap-2 alpha-1 subunit) (clathrin assembly protein complex 2 alpha-a large chain) (100 kda coated vesicle protein a) (plasma membrane adaptor ha2/ap2 adaptin alpha a subunit). [swissprot;acc:o95782]	1.09677		34	412
35.5	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	2.97183		105.5	31
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]				27
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]				40
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]				41
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]				29
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]				39
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]				30
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]				28
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]				35
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]				32
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]				37
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]				36
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]				42
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]				38
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]				33
	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]				43
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]				34
37	arf gtpase-activating protein. [refseq;acc:nm_133446]	1.78378		66	74
37	up-regulated in liver cancer 1; similar to development- and differentiation-enhancing factor 2. [refseq;acc:nm_017707]	1.78378		66	75
37.4843	suppressor of actin 1. [refseq;acc:nm_014016]	1.58781	High confidence	23.6076	89
37.693	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	1.73233		65.2968	73
39.8063	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	3.15402		12.6208	33
39.8063		3.15402	Low confidence	12.6208	25
40	probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1]	1.075	Low confidence	43	462
43	methyltransferase like 2. [refseq;acc:nm_018396]	1.3871	High confidence	31	118
	sedlin. [swissprot;acc:o14582]	4300000		0.00001	7
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	4300000		0.00001	8
47	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	29		1363	13
	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	3.04255		143	34
		3.04255	Low confidence	143	26
50	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]	1.66667	High confidence	30	81
50		1.66667	Low confidence	30	80
51	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	1.0625	High confidence	48	354
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]				350
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]				363
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]				364
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]				352
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]				362
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]				353
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]				351
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]				358
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]				355
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]				360
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]				359
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]				365
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]				361
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]				356
	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]				366

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/