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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 258 to 307 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
33	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [source:swissprot;acc:p50152]	Measured	Divided	1835.3	896.972	2.04611	
33	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Measured	Subtracted	23693.7	18263	5430.7	
33	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Squared	Subtracted	106226	192141	85915	
33	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [source:refseq;acc:nm_003690]	Rooted	Subtracted	25.6987	43.561	17.8623	
33	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [source:refseq;acc:nm_030949]	Rooted	Divided	26.0288	43.1914	1.65937	
33	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [source:swissprot;acc:p30154]	Ranked	Divided	188.688	242.742	1.28647	
33	spermatogenesis associated 6. [source:refseq;acc:nm_019073]	Squared	Divided	9924.76	25146.6	2.53372	
34	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [source:swissprot;acc:q01433]	Squared	Divided	9924.76	25146.6	2.53372	
34	gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	Rooted	Subtracted	140.508	122.878	17.63	
34	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [source:swissprot;acc:p08754]	Ranked	Subtracted	267.144	336.073	68.929	
34	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [source:swissprot;acc:p29992]	Measured	Divided	1836.71	907.546	2.02382	
34	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [source:swissprot;acc:p29992]	Rooted	Divided	40.2812	24.3678	1.65305	
34	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Measured	Subtracted	23693.7	18263	5430.7	
34	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Squared	Subtracted	106226	192141	85915	
34	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [source:swissprot;acc:p30153]	Ranked	Divided	189.07	242.453	1.28235	
35	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Squared	Divided	106226	192141	1.80879	
35	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	Rooted	Subtracted	140.508	122.878	17.63	
35	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [source:swissprot;acc:o14775]	Ranked	Subtracted	267.636	335.359	67.723	
35	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	Measured	Divided	1836.71	907.564	2.02378	
35	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	Rooted	Divided	40.2812	24.3679	1.65304	
35	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Measured	Subtracted	23693.7	18263	5430.7	
35	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Squared	Subtracted	106226	192141	85915	
35	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). [source:swissprot;acc:q13952]	Ranked	Divided	260.532	204.309	1.27519	
36	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [source:swissprot;acc:p23511]	Ranked	Divided	260.532	204.309	1.27519	
36	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [source:refseq;acc:nm_006693]	Squared	Subtracted	227160	146079	81081	
36	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [source:swissprot;acc:p19086]	Measured	Divided	1836.76	907.741	2.02344	
36	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [source:swissprot;acc:p19086]	Rooted	Divided	40.2805	24.369	1.65294	
36	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	Measured	Subtracted	23693.7	18263	5430.7	
36	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	Squared	Divided	106226	192141	1.80879	
36	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [source:refseq;acc:nm_003690]	Ranked	Subtracted	320.927	254.434	66.493	
36	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	Rooted	Subtracted	26.0288	43.1914	17.1626	
37	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [source:swissprot;acc:p04901]	Ranked	Subtracted	266.716	333.165	66.449	
37	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [source:swissprot;acc:p11488]	Measured	Divided	1836.76	907.763	2.02339	
37	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [source:swissprot;acc:p11488]	Rooted	Divided	40.2805	24.3691	1.65293	
37	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	Measured	Subtracted	23693.7	18263	5430.7	
37	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	Rooted	Subtracted	26.0288	43.1914	17.1626	
37	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Squared	Divided	106226	192141	1.80879	
37	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	Ranked	Divided	322	253	1.27273	
37	trs85 homolog. [source:swissprot;acc:q9y2l5]	Squared	Subtracted	227160	146079	81081	
38	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [source:swissprot;acc:q9hav0]	Ranked	Subtracted	266.933	333.281	66.348	
38	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [source:swissprot;acc:p19087]	Measured	Divided	1836.76	907.774	2.02337	
38	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [source:swissprot;acc:p19087]	Rooted	Divided	40.2804	24.3692	1.65292	
38	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	Measured	Subtracted	23693.7	18263	5430.7	
38	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	Ranked	Divided	322	253	1.27273	
38	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Squared	Divided	106226	192141	1.80879	
38	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	Rooted	Subtracted	26.0288	43.1914	17.1626	
38	wd-repeat protein wdc146. [source:swissprot;acc:q9c0j8]	Squared	Subtracted	226186	145568	80618	
39	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	Squared	Subtracted	226186	145568	80618	
39	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [source:swissprot;acc:q15485]	Rooted	Subtracted	26.0288	43.1914	17.1626	
39	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [source:swissprot;acc:p04899]	Measured	Divided	1836.8	907.903	2.02312	

Legend:
- Rank is the rank after comparing the two networks
- 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/