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

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Showing element 51 to 100 of 38536 in total

green	0.00001
Filtered	1
Interaction Map	High confidence
network_comparison	1
red	0.00001
Network Comparison Type	Divided

description	Value Type	Rank	
a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [source:swissprot;acc:p24588]	Squared	2788	
a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [source:swissprot;acc:p24588]	Rooted	2788	
activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [source:swissprot;acc:q04771]	Measured	3050	
activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [source:swissprot;acc:q04771]	Ranked	3050	
activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [source:swissprot;acc:q04771]	Squared	3050	
activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [source:swissprot;acc:q04771]	Rooted	3050	
adaptor protein with pleckstrin homology and src homology 2 domains. [source:refseq;acc:nm_020979]	Measured	2870	
adaptor protein with pleckstrin homology and src homology 2 domains. [source:refseq;acc:nm_020979]	Ranked	2870	
adaptor protein with pleckstrin homology and src homology 2 domains. [source:refseq;acc:nm_020979]	Squared	2870	
adaptor protein with pleckstrin homology and src homology 2 domains. [source:refseq;acc:nm_020979]	Rooted	2870	
aldehyde dehydrogenase 7 (ec 1.2.1.5). [source:swissprot;acc:p43353]	Measured	3222	
aldehyde dehydrogenase 7 (ec 1.2.1.5). [source:swissprot;acc:p43353]	Ranked	3222	
aldehyde dehydrogenase 7 (ec 1.2.1.5). [source:swissprot;acc:p43353]	Squared	3222	
aldehyde dehydrogenase 7 (ec 1.2.1.5). [source:swissprot;acc:p43353]	Rooted	3222	
aldehyde dehydrogenase 8 (ec 1.2.1.5). [source:swissprot;acc:p48448]	Measured	2992	
aldehyde dehydrogenase 8 (ec 1.2.1.5). [source:swissprot;acc:p48448]	Ranked	2992	
aldehyde dehydrogenase 8 (ec 1.2.1.5). [source:swissprot;acc:p48448]	Squared	2992	
aldehyde dehydrogenase 8 (ec 1.2.1.5). [source:swissprot;acc:p48448]	Rooted	2992	
aldehyde oxidase (ec 1.2.3.1). [source:swissprot;acc:q06278]	Measured	2960	
aldehyde oxidase (ec 1.2.3.1). [source:swissprot;acc:q06278]	Ranked	2960	
aldehyde oxidase (ec 1.2.3.1). [source:swissprot;acc:q06278]	Squared	2960	
aldehyde oxidase (ec 1.2.3.1). [source:swissprot;acc:q06278]	Rooted	2960	
alpha crystallin a chain. [source:swissprot;acc:p02489]	Measured	2875	
alpha crystallin a chain. [source:swissprot;acc:p02489]	Ranked	2875	
alpha crystallin a chain. [source:swissprot;acc:p02489]	Squared	2875	
alpha crystallin a chain. [source:swissprot;acc:p02489]	Rooted	2875	
alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [source:swissprot;acc:p02511]	Measured	3082	
alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [source:swissprot;acc:p02511]	Ranked	3082	
alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [source:swissprot;acc:p02511]	Squared	3082	
alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [source:swissprot;acc:p02511]	Rooted	3082	
alveolar soft part sarcoma chromosome region, candidate 1; aspl protein; renal cell carcinoma gene on chromosome 17; renal cell carcinoma, papillary, 17 gene; aspscr1/tfe3 fusion gene, included. [source:refseq;acc:nm_024083]	Measured	2829	
alveolar soft part sarcoma chromosome region, candidate 1; aspl protein; renal cell carcinoma gene on chromosome 17; renal cell carcinoma, papillary, 17 gene; aspscr1/tfe3 fusion gene, included. [source:refseq;acc:nm_024083]	Ranked	2829	
alveolar soft part sarcoma chromosome region, candidate 1; aspl protein; renal cell carcinoma gene on chromosome 17; renal cell carcinoma, papillary, 17 gene; aspscr1/tfe3 fusion gene, included. [source:refseq;acc:nm_024083]	Squared	2829	
alveolar soft part sarcoma chromosome region, candidate 1; aspl protein; renal cell carcinoma gene on chromosome 17; renal cell carcinoma, papillary, 17 gene; aspscr1/tfe3 fusion gene, included. [source:refseq;acc:nm_024083]	Rooted	2829	
amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [source:refseq;acc:nm_006380]	Measured	3191	
amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [source:refseq;acc:nm_006380]	Ranked	3191	
amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [source:refseq;acc:nm_006380]	Squared	3191	
amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [source:refseq;acc:nm_006380]	Rooted	3191	
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [source:swissprot;acc:o95376]	Measured	2798	
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [source:swissprot;acc:o95376]	Ranked	2798	
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [source:swissprot;acc:o95376]	Squared	2798	
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [source:swissprot;acc:o95376]	Rooted	2798	
atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [source:swissprot;acc:p18859]	Measured	2893	
atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [source:swissprot;acc:p18859]	Ranked	2893	
atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [source:swissprot;acc:p18859]	Squared	2893	
atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [source:swissprot;acc:p18859]	Rooted	2893	
atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [source:swissprot;acc:o75964]	Measured	2834	
atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [source:swissprot;acc:o75964]	Ranked	2834	
atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [source:swissprot;acc:o75964]	Squared	2834	
atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [source:swissprot;acc:o75964]	Rooted	2834	

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/