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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 1 to 32 of 32 in total

Rank  : 12

description	Filtered	Value Type	Interaction Map	Network Comparison Type	green	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	Subtracted	34.6716	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	Divided	1933	1.65028	3190
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		Squared	High confidence	Subtracted	19295.9	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			Divided	1281.5	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	Subtracted	336.233	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	Divided	5.71669	34.8539	199.249
		Ranked	Low confidence	Subtracted	21113.7	6521.7	14592
		Squared		Divided	0.0297673	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	Subtracted	129762	89286	219048
mitochondrial solute carrier protein. [refseq;acc:nm_145305]			Low confidence	Divided	192141	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	Subtracted	40795.8	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	Divided	232	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			Subtracted	11267	8136	19403
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]		Squared		Divided	0.437633	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	Subtracted	30022.4	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		Divided	47.9763	1.48549	32.2966
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]		Ranked			28.5242	1.30933	37.3475
		Rooted		Subtracted	204.557	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.