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 Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 25 to 74 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Ranked	Divided	15	28	1.86667	
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Squared	Subtracted	407289	263351	143938	
4	cytohesin 4. [source:swissprot;acc:q9uia0]	Measured	Subtracted	41482.5	33356.5	8126	
4	hbs1-like. [source:refseq;acc:nm_006620]	Measured	Divided	2597.5	698.5	3.71868	
4	hbs1-like. [source:refseq;acc:nm_006620]	Squared	Divided	1596.92	115.48	13.8285	
4	hbs1-like. [source:refseq;acc:nm_006620]	Rooted	Divided	50.9657	26.4292	1.92839	
4	hbs1-like. [source:refseq;acc:nm_006620]	Rooted	Subtracted	50.9657	26.4292	24.5365	
4	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Ranked	Subtracted	337	232	105	
5	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Rooted	Subtracted	145.551	168.796	23.245	
5	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Measured	Subtracted	41482.5	33356.5	8126	
5	cytohesin 4. [source:swissprot;acc:q9uia0]	Ranked	Divided	15	28	1.86667	
5	cytohesin 4. [source:swissprot;acc:q9uia0]	Squared	Subtracted	407289	263351	143938	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Measured	Divided	1153.5	339.5	3.39764	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Squared	Divided	314.926	27.2805	11.544	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Rooted	Divided	33.9632	18.4255	1.84327	
5	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Ranked	Subtracted	212	309	97	
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Ranked	Divided	15	28	1.86667	
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Squared	Subtracted	407289	263351	143938	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Measured	Divided	1153.5	339.5	3.39764	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Squared	Divided	314.926	27.2805	11.544	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Rooted	Divided	33.9632	18.4255	1.84327	
6	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	Rooted	Subtracted	145.551	168.796	23.245	
6	protein x 0004. [source:refseq;acc:nm_016301]	Ranked	Subtracted	212	309	97	
6	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Measured	Subtracted	44490.5	36927.5	7563	
7	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Measured	Subtracted	21185	28492	7307	
7	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Ranked	Divided	215	322	1.49767	
7	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Squared	Subtracted	310840	442993	132153	
7	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Rooted	Subtracted	145.551	168.796	23.245	
7	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Ranked	Subtracted	288.754	212.554	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	1153.5	339.5	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	314.926	27.2805	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	33.9632	18.4255	1.84327	
8	db83 protein. [source:swissprot;acc:p57088]	Measured	Divided	1153.5	339.5	3.39764	
8	db83 protein. [source:swissprot;acc:p57088]	Squared	Divided	314.926	27.2805	11.544	
8	db83 protein. [source:swissprot;acc:p57088]	Rooted	Divided	33.9632	18.4255	1.84327	
8	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Squared	Subtracted	250303	354894	104591	
8	hbs1-like. [source:refseq;acc:nm_006620]	Ranked	Divided	215	322	1.49767	
8	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Ranked	Subtracted	288	362	74	
8	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	Measured	Subtracted	21185	28492	7307	
8	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Rooted	Subtracted	145.551	168.796	23.245	
9	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Ranked	Subtracted	288	362	74	
9	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Rooted	Subtracted	145.551	168.796	23.245	
9	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Measured	Subtracted	21185	28492	7307	
9	protein phosphatase 1, regulatory subunit 7; sds22. [source:refseq;acc:nm_002712]	Squared	Subtracted	256169	162517	93652	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Measured	Divided	398.5	1281.5	3.21581	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Squared	Divided	37.5863	388.696	10.3414	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Rooted	Divided	19.9625	35.798	1.79326	
9	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Ranked	Divided	212	309	1.45755	
10	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [source:refseq;acc:nm_030801]	Squared	Subtracted	219048	129762	89286	
10	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Measured	Subtracted	21185	28492	7307	

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/