MK5 Microarray Data

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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 32 of 32 in total

Rank  : 12

description	Filtered	Value Type	Interaction Map	green	Network Comparison Type	network_comparison	red
adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	0	Rooted	High confidence	34.6716	Subtracted	13.2749	21.3967
anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]		Ranked	Low confidence	1933	Divided	1.65028	3190
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		Squared	High confidence	19295.9	Subtracted	19294.2	1.73869
bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061]	1		Low confidence	228277		53522	281799
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]		Rooted	High confidence	101.526		21.0555	80.4705
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	0		Low confidence	11.7898		12.0849	23.8747
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]		Measured	High confidence	7099.51		1469.89	5629.62
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	1			1281.5	Divided	3.21581	398.5
		Squared		388.696		10.3414	37.5863
		Rooted		35.798		1.79326	19.9625
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	0	Ranked		5208.84		1.81023	9429.18
gbp protein isoform a. [refseq;acc:nm_017870]	1	Measured	Low confidence	2954.24		1.5371	1921.96
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]		Ranked	High confidence	336.233	Subtracted	69.377	266.856
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Measured	Low confidence	17572.7		2108.6	15464.1
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	0		High confidence	5.71669	Divided	34.8539	199.249
		Ranked	Low confidence	21113.7	Subtracted	6521.7	14592
		Squared		0.0297673	Divided	789.312	23.4957
		Rooted		1.2188		8.45791	10.3085
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	1	Squared	High confidence	129762	Subtracted	89286	219048
mitochondrial solute carrier protein. [refseq;acc:nm_145305]			Low confidence	192141	Divided	1.80879	106226
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	Measured		58		14.8103	859
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	1		High confidence	40795.8	Subtracted	6604.9	34190.9
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	0	Squared	Low confidence	23426.5		12936.7	10489.8
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	Ranked	High confidence	232	Divided	1.45259	337
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	0			11267	Subtracted	8136	19403
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]		Squared		0.437633	Divided	43763.3	0.00001
		Rooted		6.55744		655744
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]		Measured	Low confidence	30022.4	Subtracted	1099.6	31122
trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477]	1	Ranked		246.737		57.622	304.359
		Rooted		47.9763	Divided	1.48549	32.2966
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]		Ranked		28.5242		1.30933	37.3475
		Rooted		204.557	Subtracted	17.232	187.325

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.