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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 275 to 324 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	description	Network Comparison Type	red	network_comparison	green
35	Ranked	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]	Subtracted	267.636	67.723	335.359
		nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	Divided	260.532	1.27519	204.309
	Squared	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		106226	1.80879	192141
		mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Subtracted		85915
	Rooted	apg3p; pc3-96 protein. [refseq;acc:nm_022488]		140.508	17.63	122.878
		guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	Divided	40.2812	1.65304	24.3679
36	Measured	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]		1836.76	2.02344	907.741
		melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Subtracted	23693.7	5430.7	18263
	Ranked	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	Divided	260.532	1.27519	204.309
		protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Subtracted	320.927	66.493	254.434
	Squared	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]		227160	81081	146079
		pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Divided	106226	1.80879	192141
	Rooted	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]		40.2805	1.65294	24.369
		protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Subtracted	26.0288	17.1626	43.1914
37	Measured	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	Divided	1836.76	2.02339	907.763
		melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Subtracted	23693.7	5430.7	18263
	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]		266.716	66.449	333.165
		protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Divided	322	1.27273	253
	Squared	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]		106226	1.80879	192141
		trs85 homolog. [swissprot;acc:q9y2l5]	Subtracted	227160	81081	146079
	Rooted	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	Divided	40.2805	1.65293	24.3691
		microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Subtracted	26.0288	17.1626	43.1914
38	Measured	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	Divided	1836.76	2.02337	907.774
		melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Subtracted	23693.7	5430.7	18263
	Ranked	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]		266.933	66.348	333.281
		microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Divided	322	1.27273	253
	Squared	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]		106226	1.80879	192141
		wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	Subtracted	226186	80618	145568
	Rooted	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	Divided	40.2804	1.65292	24.3692
		protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Subtracted	26.0288	17.1626	43.1914
39	Measured	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	Divided	1836.8	2.02312	907.903
		melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Subtracted	23693.7	5430.7	18263
	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]		268.565	65.918	334.483
		protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Divided	322	1.27273	253
	Squared	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Subtracted	226186	80618	145568
		mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Divided	106226	1.80879	192141
	Rooted	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Subtracted	26.0288	17.1626	43.1914
		guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	Divided	40.28	1.65285	24.37
40	Measured	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]		1836.81	2.02297	907.978
		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]	Subtracted	23693.7	5430.7	18263
	Ranked	deltex 2. [refseq;acc:nm_020892]		333.144	65.751	267.393
		ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Divided	322	1.27273	253
	Squared	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	Subtracted	222655	79071	143584
		cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Divided	144940	1.78564	81169.7
	Rooted	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]		40.2797	1.65281	24.3705
		protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Subtracted	26.0288	17.1626	43.1914
41	Measured	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]	Divided	1836.81	2.02297	907.978
		trophinin. [swissprot;acc:q12816]	Subtracted	23693.7	5430.7	18263
	Ranked	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]		332.925	65.651	267.274
		protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Divided	322	1.27273	253

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.