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 177 to 226 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
23	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Ranked	Divided	58	44	1.31818	
23	gbp protein isoform a. [source:refseq;acc:nm_017870]	Measured	Divided	699.76	1894.39	2.7072	
23	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [source:swissprot;acc:p29798]	Rooted	Divided	40.3358	24.2919	1.66046	
23	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	Measured	Subtracted	23693.7	18263	5430.7	
23	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Squared	Subtracted	219048	129762	89286	
23	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	Ranked	Subtracted	322	253	69	
23	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	Rooted	Subtracted	153.578	133.176	20.402	
23	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	Squared	Divided	143.692	457.521	3.18404	
24	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [source:swissprot;acc:q12873]	Squared	Divided	143.692	457.521	3.18404	
24	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Rooted	Subtracted	153.548	133.153	20.395	
24	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [source:swissprot;acc:q9uk08]	Rooted	Divided	40.336	24.2941	1.66032	
24	melanoma-associated antigen 11 (mage-11 antigen). [source:swissprot;acc:p43364]	Measured	Subtracted	23693.7	18263	5430.7	
24	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Squared	Subtracted	219048	129762	89286	
24	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	Ranked	Divided	58	44	1.31818	
24	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [source:refseq;acc:nm_003690]	Measured	Divided	950.561	2108.52	2.21818	
24	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	Ranked	Subtracted	322	253	69	
25	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	Squared	Divided	143.692	457.521	3.18404	
25	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]	Ranked	Subtracted	322	253	69	
25	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [source:swissprot;acc:p30670]	Rooted	Divided	40.3361	24.295	1.66026	
25	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [source:swissprot;acc:o60262]	Measured	Divided	1833.01	892.67	2.0534	
25	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	Squared	Subtracted	219048	129762	89286	
25	melanoma-associated antigen 2 (mage-2 antigen). [source:swissprot;acc:p43356]	Measured	Subtracted	23693.7	18263	5430.7	
25	myosin vb (myosin 5b) (fragment). [source:swissprot;acc:q9ulv0]	Rooted	Subtracted	146.94	167.046	20.106	
25	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Ranked	Divided	58	44	1.31818	
26	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [source:swissprot;acc:p50151]	Rooted	Divided	40.3362	24.2954	1.66024	
26	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [source:swissprot;acc:q9ubi6]	Measured	Divided	1833.01	892.67	2.0534	
26	hepatocellular carcinoma-associated protein hca1. [source:refseq;acc:nm_020932]	Measured	Subtracted	23693.7	18263	5430.7	
26	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	Squared	Subtracted	219048	129762	89286	
26	myosin vc (myosin 5c). [source:swissprot;acc:q9nqx4]	Rooted	Subtracted	146.94	167.046	20.106	
26	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	Squared	Divided	143.692	457.521	3.18404	
26	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Ranked	Divided	58	44	1.31818	
26	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]	Ranked	Subtracted	322	253	69	
27	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [source:swissprot;acc:p50150]	Measured	Divided	1834.33	895.134	2.04922	
27	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [source:swissprot;acc:q9y3k8]	Rooted	Divided	40.3364	24.2968	1.66015	
27	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	Ranked	Subtracted	267.136	336.077	68.941	
27	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	Squared	Subtracted	219048	129762	89286	
27	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]	Measured	Subtracted	23693.7	18263	5430.7	
27	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Ranked	Divided	58	44	1.31818	
27	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	Rooted	Subtracted	146.94	167.046	20.106	
27	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	Squared	Divided	143.692	457.521	3.18404	
28	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [source:swissprot;acc:p18847]	Ranked	Divided	201.949	153.671	1.31416	
28	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	Rooted	Subtracted	149.165	129.699	19.466	
28	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [source:swissprot;acc:p50152]	Rooted	Divided	40.3372	24.3043	1.65967	
28	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [source:swissprot;acc:p29798]	Measured	Divided	1834.36	895.194	2.04912	
28	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [source:swissprot;acc:p29992]	Ranked	Subtracted	267.136	336.077	68.941	
28	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	Squared	Subtracted	219048	129762	89286	
28	necdin. [source:swissprot;acc:q99608]	Measured	Subtracted	23693.7	18263	5430.7	
28	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	Squared	Divided	143.692	457.521	3.18404	
29	chromodomain helicase dna binding protein 5. [source:refseq;acc:nm_015557]	Squared	Divided	143.692	457.521	3.18404	
29	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [source:swissprot;acc:q9uk08]	Measured	Divided	1834.52	895.507	2.04858	

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/