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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	Value Type	description	Network Comparison Type	red	green	network_comparison	
7	Ranked	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Divided	215	322	1.49767	
7	Ranked	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Subtracted	288.754	212.554	76.2	
7	Squared	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Subtracted	310840	442993	132153	
7	Squared	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]	Divided	314.926	27.2805	11.544	
7	Rooted	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Subtracted	145.551	168.796	23.245	
7	Rooted	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]	Divided	33.9632	18.4255	1.84327	
8	Measured	db83 protein. [source:swissprot;acc:p57088]	Divided	1153.5	339.5	3.39764	
8	Measured	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	Subtracted	21185	28492	7307	
8	Ranked	hbs1-like. [source:refseq;acc:nm_006620]	Divided	215	322	1.49767	
8	Ranked	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Subtracted	288	362	74	
8	Squared	db83 protein. [source:swissprot;acc:p57088]	Divided	314.926	27.2805	11.544	
8	Squared	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Subtracted	250303	354894	104591	
8	Rooted	db83 protein. [source:swissprot;acc:p57088]	Divided	33.9632	18.4255	1.84327	
8	Rooted	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Subtracted	145.551	168.796	23.245	
9	Measured	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Subtracted	21185	28492	7307	
9	Measured	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Divided	398.5	1281.5	3.21581	
9	Ranked	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Subtracted	288	362	74	
9	Ranked	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Divided	212	309	1.45755	
9	Squared	protein phosphatase 1, regulatory subunit 7; sds22. [source:refseq;acc:nm_002712]	Subtracted	256169	162517	93652	
9	Squared	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Divided	37.5863	388.696	10.3414	
9	Rooted	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Subtracted	145.551	168.796	23.245	
9	Rooted	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Divided	19.9625	35.798	1.79326	
10	Measured	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Subtracted	21185	28492	7307	
10	Measured	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Divided	398.5	1281.5	3.21581	
10	Ranked	protein x 0004. [source:refseq;acc:nm_016301]	Divided	212	309	1.45755	
10	Ranked	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]	Subtracted	288	362	74	
10	Squared	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [source:refseq;acc:nm_030801]	Subtracted	219048	129762	89286	
10	Squared	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Divided	37.5863	388.696	10.3414	
10	Rooted	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Divided	19.9625	35.798	1.79326	
10	Rooted	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Subtracted	51.6817	29.5127	22.169	
11	Measured	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Divided	398.5	1281.5	3.21581	
11	Measured	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Subtracted	21185	28492	7307	
11	Ranked	db83 protein. [source:swissprot;acc:p57088]	Subtracted	288	362	74	
11	Ranked	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Divided	337	232	1.45259	
11	Squared	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Divided	37.5863	388.696	10.3414	
11	Squared	hepatocellular carcinoma-associated protein hca3. [source:refseq;acc:nm_138703]	Subtracted	219048	129762	89286	
11	Rooted	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Divided	19.9625	35.798	1.79326	
11	Rooted	protein x 0004. [source:refseq;acc:nm_016301]	Subtracted	51.6817	29.5127	22.169	
12	Measured	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Divided	398.5	1281.5	3.21581	
12	Measured	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Subtracted	34190.9	40795.8	6604.9	
12	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [source:swissprot;acc:o60262]	Subtracted	266.856	336.233	69.377	
12	Ranked	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Divided	337	232	1.45259	
12	Squared	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Divided	37.5863	388.696	10.3414	
12	Squared	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	Subtracted	219048	129762	89286	
12	Rooted	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Subtracted	80.4705	101.526	21.0555	
12	Rooted	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Divided	19.9625	35.798	1.79326	
13	Measured	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Divided	398.5	1281.5	3.21581	
13	Measured	myosin vb (myosin 5b) (fragment). [source:swissprot;acc:q9ulv0]	Subtracted	21591.5	27904.5	6313	
13	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [source:swissprot;acc:q9ubi6]	Subtracted	266.856	336.233	69.377	
13	Ranked	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Divided	288.754	212.554	1.3585	

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/