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 100 to 149 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
13	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Rooted	Divided	19.9625	35.798	1.79326	
13	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [source:swissprot;acc:q9ubi6]	Ranked	Subtracted	266.856	336.233	69.377	
13	melanoma-associated antigen 11 (mage-11 antigen). [source:swissprot;acc:p43364]	Squared	Subtracted	219048	129762	89286	
13	myosin vb (myosin 5b) (fragment). [source:swissprot;acc:q9ulv0]	Measured	Subtracted	21591.5	27904.5	6313	
13	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Ranked	Divided	288.754	212.554	1.3585	
14	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Ranked	Divided	56.6768	75.3531	1.32952	
14	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [source:swissprot;acc:p50150]	Ranked	Subtracted	266.863	336.191	69.328	
14	melanoma-associated antigen 2 (mage-2 antigen). [source:swissprot;acc:p43356]	Squared	Subtracted	219048	129762	89286	
14	myosin vc (myosin 5c). [source:swissprot;acc:q9nqx4]	Measured	Subtracted	21591.5	27904.5	6313	
14	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	Measured	Divided	398.5	1281.5	3.21581	
14	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	Squared	Divided	37.5863	388.696	10.3414	
14	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	Rooted	Divided	19.9625	35.798	1.79326	
14	spermatogenesis associated 6. [source:refseq;acc:nm_019073]	Rooted	Subtracted	80.4705	101.526	21.0555	
15	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [source:swissprot;acc:q01433]	Rooted	Subtracted	80.4705	101.526	21.0555	
15	gbp protein isoform a. [source:refseq;acc:nm_017870]	Rooted	Divided	23.9771	42.4773	1.77158	
15	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [source:swissprot;acc:p29798]	Ranked	Subtracted	266.863	336.19	69.327	
15	hepatocellular carcinoma-associated protein hca1. [source:refseq;acc:nm_020932]	Squared	Subtracted	219048	129762	89286	
15	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	Ranked	Divided	56.7244	75.3948	1.32914	
15	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	Measured	Subtracted	21591.5	27904.5	6313	
15	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Measured	Divided	2671	871	3.06659	
15	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Squared	Divided	1688.58	179.56	9.40399	
16	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Measured	Subtracted	24260.3	18172.1	6088.2	
16	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [source:swissprot;acc:q9uk08]	Ranked	Subtracted	266.864	336.184	69.32	
16	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [source:swissprot;acc:o60476]	Rooted	Subtracted	203.673	182.638	21.035	
16	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]	Squared	Subtracted	219048	129762	89286	
16	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	Ranked	Divided	56.7252	75.3954	1.32913	
16	protein x 0004. [source:refseq;acc:nm_016301]	Measured	Divided	2671	871	3.06659	
16	protein x 0004. [source:refseq;acc:nm_016301]	Squared	Divided	1688.58	179.56	9.40399	
16	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Rooted	Divided	51.6817	29.5127	1.75117	
17	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Ranked	Divided	56.7841	75.447	1.32866	
17	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Rooted	Subtracted	203.673	182.638	21.035	
17	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	Measured	Divided	460	1365	2.96739	
17	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	Squared	Divided	50.0828	441	8.80542	
17	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [source:swissprot;acc:p30670]	Ranked	Subtracted	266.864	336.182	69.318	
17	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	Measured	Subtracted	24255.7	18168.9	6086.8	
17	necdin. [source:swissprot;acc:q99608]	Squared	Subtracted	219048	129762	89286	
17	protein x 0004. [source:refseq;acc:nm_016301]	Rooted	Divided	51.6817	29.5127	1.75117	
18	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Ranked	Divided	185.678	245.247	1.32082	
18	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Rooted	Subtracted	203.673	182.638	21.035	
18	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	Rooted	Divided	21.4476	36.9459	1.72261	
18	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [source:swissprot;acc:p50151]	Ranked	Subtracted	266.865	336.181	69.316	
18	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	Squared	Subtracted	219048	129762	89286	
18	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	Measured	Subtracted	24255.7	18168.9	6086.8	
18	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	Measured	Divided	677.5	1865.5	2.75351	
18	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	Squared	Divided	108.641	823.69	7.58176	
19	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Measured	Subtracted	24250	18164.9	6085.1	
19	cytohesin 4. [source:swissprot;acc:q9uia0]	Rooted	Subtracted	203.673	182.638	21.035	
19	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Ranked	Divided	185.678	245.247	1.32082	
19	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [source:swissprot;acc:q9y3k8]	Ranked	Subtracted	266.865	336.178	69.313	
19	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	Squared	Subtracted	219048	129762	89286	

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/