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.

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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 25824 in total

Filtered	1
Interaction Map	High confidence

Rank	description	Value Type	Network Comparison Type	green	red	network_comparison	
7	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Squared	Subtracted	442993	310840	132153	
7	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Rooted	Subtracted	168.796	145.551	23.245	
7	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Ranked	Subtracted	212.554	288.754	76.2	
7	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	Measured	Divided	339.5	1153.5	3.39764	
7	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	Squared	Divided	27.2805	314.926	11.544	
7	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	Rooted	Divided	18.4255	33.9632	1.84327	
8	db83 protein. [source:swissprot;acc:p57088]	Measured	Divided	339.5	1153.5	3.39764	
8	db83 protein. [source:swissprot;acc:p57088]	Squared	Divided	27.2805	314.926	11.544	
8	db83 protein. [source:swissprot;acc:p57088]	Rooted	Divided	18.4255	33.9632	1.84327	
8	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Squared	Subtracted	354894	250303	104591	
8	hbs1-like. [source:refseq;acc:nm_006620]	Ranked	Divided	322	215	1.49767	
8	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Ranked	Subtracted	362	288	74	
8	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	Measured	Subtracted	28492	21185	7307	
8	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Rooted	Subtracted	168.796	145.551	23.245	
9	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Ranked	Subtracted	362	288	74	
9	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Rooted	Subtracted	168.796	145.551	23.245	
9	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Measured	Subtracted	28492	21185	7307	
9	protein phosphatase 1, regulatory subunit 7; sds22. [source:refseq;acc:nm_002712]	Squared	Subtracted	162517	256169	93652	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Measured	Divided	1281.5	398.5	3.21581	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Squared	Divided	388.696	37.5863	10.3414	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Rooted	Divided	35.798	19.9625	1.79326	
9	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Ranked	Divided	309	212	1.45755	
10	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [source:refseq;acc:nm_030801]	Squared	Subtracted	129762	219048	89286	
10	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Measured	Subtracted	28492	21185	7307	
10	protein x 0004. [source:refseq;acc:nm_016301]	Ranked	Divided	309	212	1.45755	
10	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	Ranked	Subtracted	362	288	74	
10	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Measured	Divided	1281.5	398.5	3.21581	
10	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Squared	Divided	388.696	37.5863	10.3414	
10	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Rooted	Divided	35.798	19.9625	1.79326	
10	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Rooted	Subtracted	29.5127	51.6817	22.169	
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Measured	Divided	1281.5	398.5	3.21581	
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Squared	Divided	388.696	37.5863	10.3414	
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Rooted	Divided	35.798	19.9625	1.79326	
11	db83 protein. [source:swissprot;acc:p57088]	Ranked	Subtracted	362	288	74	
11	hepatocellular carcinoma-associated protein hca3. [source:refseq;acc:nm_138703]	Squared	Subtracted	129762	219048	89286	
11	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Measured	Subtracted	28492	21185	7307	
11	protein x 0004. [source:refseq;acc:nm_016301]	Rooted	Subtracted	29.5127	51.6817	22.169	
11	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Ranked	Divided	232	337	1.45259	
12	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Rooted	Subtracted	101.526	80.4705	21.0555	
12	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Measured	Divided	1281.5	398.5	3.21581	
12	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Squared	Divided	388.696	37.5863	10.3414	
12	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Rooted	Divided	35.798	19.9625	1.79326	
12	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [source:swissprot;acc:o60262]	Ranked	Subtracted	336.233	266.856	69.377	
12	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	Squared	Subtracted	129762	219048	89286	
12	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Measured	Subtracted	40795.8	34190.9	6604.9	
12	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Ranked	Divided	232	337	1.45259	
13	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Rooted	Subtracted	101.526	80.4705	21.0555	
13	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Measured	Divided	1281.5	398.5	3.21581	
13	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Squared	Divided	388.696	37.5863	10.3414	
13	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Rooted	Divided	35.798	19.9625	1.79326	

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/