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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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 501 to 550 of 1892 in total

Network Comparison Type	Subtracted
Interaction Map	High confidence
Filtered	1
red	0
green	0
network_comparison	0

Rank	description	Value Type	
2881	collectin sub-family member 12 isoform i; scavenger receptor with c-type lectin; collectin placenta 1; scavenger receptor class a, member 4. [source:refseq;acc:nm_130386]	Measured	
2881	collectin sub-family member 12 isoform i; scavenger receptor with c-type lectin; collectin placenta 1; scavenger receptor class a, member 4. [source:refseq;acc:nm_130386]	Ranked	
2881	collectin sub-family member 12 isoform i; scavenger receptor with c-type lectin; collectin placenta 1; scavenger receptor class a, member 4. [source:refseq;acc:nm_130386]	Squared	
2881	collectin sub-family member 12 isoform i; scavenger receptor with c-type lectin; collectin placenta 1; scavenger receptor class a, member 4. [source:refseq;acc:nm_130386]	Rooted	
2882	xanthine dehydrogenase/oxidase [includes: xanthine dehydrogenase (ec 1.1.1.204) (xd); xanthine oxidase (ec 1.1.3.22) (xo) (xanthine oxidoreductase)]. [source:swissprot;acc:p47989]	Measured	
2882	xanthine dehydrogenase/oxidase [includes: xanthine dehydrogenase (ec 1.1.1.204) (xd); xanthine oxidase (ec 1.1.3.22) (xo) (xanthine oxidoreductase)]. [source:swissprot;acc:p47989]	Ranked	
2882	xanthine dehydrogenase/oxidase [includes: xanthine dehydrogenase (ec 1.1.1.204) (xd); xanthine oxidase (ec 1.1.3.22) (xo) (xanthine oxidoreductase)]. [source:swissprot;acc:p47989]	Squared	
2882	xanthine dehydrogenase/oxidase [includes: xanthine dehydrogenase (ec 1.1.1.204) (xd); xanthine oxidase (ec 1.1.3.22) (xo) (xanthine oxidoreductase)]. [source:swissprot;acc:p47989]	Rooted	
2883	pantothenate kinase 4 (ec 2.7.1.33) (pantothenic acid kinase 4) (hpank4). [source:swissprot;acc:q9nve7]	Measured	
2883	pantothenate kinase 4 (ec 2.7.1.33) (pantothenic acid kinase 4) (hpank4). [source:swissprot;acc:q9nve7]	Ranked	
2883	pantothenate kinase 4 (ec 2.7.1.33) (pantothenic acid kinase 4) (hpank4). [source:swissprot;acc:q9nve7]	Squared	
2883	pantothenate kinase 4 (ec 2.7.1.33) (pantothenic acid kinase 4) (hpank4). [source:swissprot;acc:q9nve7]	Rooted	
2884	peptide deformylase, mitochondrial precursor (ec 3.5.1.88) (pdf) (polypeptide deformylase). [source:swissprot;acc:q9hbh1]	Measured	
2884	peptide deformylase, mitochondrial precursor (ec 3.5.1.88) (pdf) (polypeptide deformylase). [source:swissprot;acc:q9hbh1]	Ranked	
2884	peptide deformylase, mitochondrial precursor (ec 3.5.1.88) (pdf) (polypeptide deformylase). [source:swissprot;acc:q9hbh1]	Squared	
2884	peptide deformylase, mitochondrial precursor (ec 3.5.1.88) (pdf) (polypeptide deformylase). [source:swissprot;acc:q9hbh1]	Rooted	
2885	carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [source:swissprot;acc:p23786]	Measured	
2885	carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [source:swissprot;acc:p23786]	Ranked	
2885	carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [source:swissprot;acc:p23786]	Squared	
2885	carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [source:swissprot;acc:p23786]	Rooted	
2886	complement component c8 alpha chain precursor. [source:swissprot;acc:p07357]	Measured	
2886	complement component c8 alpha chain precursor. [source:swissprot;acc:p07357]	Ranked	
2886	complement component c8 alpha chain precursor. [source:swissprot;acc:p07357]	Squared	
2886	complement component c8 alpha chain precursor. [source:swissprot;acc:p07357]	Rooted	
2887	mothers against decapentaplegic homolog interacting protein (madh-interacting protein) (smad anchor for receptor activation) (receptor activation anchor) (hsara) (novel serine protease) (nsp). [source:swissprot;acc:o95405]	Measured	
2887	mothers against decapentaplegic homolog interacting protein (madh-interacting protein) (smad anchor for receptor activation) (receptor activation anchor) (hsara) (novel serine protease) (nsp). [source:swissprot;acc:o95405]	Ranked	
2887	mothers against decapentaplegic homolog interacting protein (madh-interacting protein) (smad anchor for receptor activation) (receptor activation anchor) (hsara) (novel serine protease) (nsp). [source:swissprot;acc:o95405]	Squared	
2887	mothers against decapentaplegic homolog interacting protein (madh-interacting protein) (smad anchor for receptor activation) (receptor activation anchor) (hsara) (novel serine protease) (nsp). [source:swissprot;acc:o95405]	Rooted	
2888	eukaryotic initiation factor 4a-ii (eif-4a-ii) (eif4a-ii). [source:swissprot;acc:q14240]	Measured	
2888	eukaryotic initiation factor 4a-ii (eif-4a-ii) (eif4a-ii). [source:swissprot;acc:q14240]	Ranked	
2888	eukaryotic initiation factor 4a-ii (eif-4a-ii) (eif4a-ii). [source:swissprot;acc:q14240]	Squared	
2888	eukaryotic initiation factor 4a-ii (eif-4a-ii) (eif4a-ii). [source:swissprot;acc:q14240]	Rooted	
2889	udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [source:swissprot;acc:p06133]	Measured	
2889	udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [source:swissprot;acc:p06133]	Ranked	
2889	udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [source:swissprot;acc:p06133]	Squared	
2889	udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [source:swissprot;acc:p06133]	Rooted	
2890	ccr4-not transcription complex, subunit 8 (caf1-like protein) (califp). [source:swissprot;acc:q9uff9]	Measured	
2890	ccr4-not transcription complex, subunit 8 (caf1-like protein) (califp). [source:swissprot;acc:q9uff9]	Ranked	
2890	ccr4-not transcription complex, subunit 8 (caf1-like protein) (califp). [source:swissprot;acc:q9uff9]	Squared	
2890	ccr4-not transcription complex, subunit 8 (caf1-like protein) (califp). [source:swissprot;acc:q9uff9]	Rooted	
2891	putative mitochondrial solute carrier; hypothetical protein npd016; putative mitochondrial solute carrier. [source:refseq;acc:nm_031212]	Measured	
2891	putative mitochondrial solute carrier; hypothetical protein npd016; putative mitochondrial solute carrier. [source:refseq;acc:nm_031212]	Ranked	
2891	putative mitochondrial solute carrier; hypothetical protein npd016; putative mitochondrial solute carrier. [source:refseq;acc:nm_031212]	Squared	
2891	putative mitochondrial solute carrier; hypothetical protein npd016; putative mitochondrial solute carrier. [source:refseq;acc:nm_031212]	Rooted	
2892	cyclin-dependent kinase (cdc2-like) 11; death-preventing kinase. [source:refseq;acc:nm_015076]	Measured	
2892	cyclin-dependent kinase (cdc2-like) 11; death-preventing kinase. [source:refseq;acc:nm_015076]	Ranked	
2892	cyclin-dependent kinase (cdc2-like) 11; death-preventing kinase. [source:refseq;acc:nm_015076]	Squared	
2892	cyclin-dependent kinase (cdc2-like) 11; death-preventing kinase. [source:refseq;acc:nm_015076]	Rooted	
2893	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	

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/