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 3908 to 3957 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1954 probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Divided 5888.32 6245.89 1.06073
1955 28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] 5195.3 5510.67 1.0607
eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] Subtracted 5490.24 5838.67 348.43
1956 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] 5475.44 5127.66 347.78
nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062] Divided 4689.78 4973.44 1.06048
1957 kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066] Subtracted 5934.08 6281.2 347.12
transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] Divided 7019.78 7444.06 1.06044
1958 baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] Subtracted 5976.81 6323.87 347.06
splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [refseq;acc:nm_016333] Divided 5448.35 5777.35 1.06039
1959 kinesin-like protein kif3c. [swissprot;acc:o14782] Subtracted 5934.68 6281.49 346.81
splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [swissprot;acc:q01081] Divided 5448.35 5777.35 1.06039
1960 hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] Subtracted 5567.41 5914.05 346.64
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Divided 5448.35 5777.35 1.06039
1961 bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] Subtracted 5830.46 6176.71 346.25
splicing factor u2af 65 kda subunit (u2 auxiliary factor 65 kda subunit) (u2 snrnp auxiliary factor large subunit) (hu2af(65)). [swissprot;acc:p26368] Divided 5448.35 5777.35 1.06039
1962 c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [swissprot;acc:q9upt6] 5941.24 6297.78 1.06001
peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] Subtracted 5830.03 6176.1 346.07
1963 peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] 5829.74 6175.69 345.95
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Divided 4374.32 4126.96 1.05994
1964 brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] Subtracted 5669.9 6015.75 345.85
pp3111 protein. [refseq;acc:nm_022156] Divided 4374.32 4126.96 1.05994
1965 dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] Subtracted 4619.81 4965.45 345.64
syntaxin 18. [swissprot;acc:q9p2w9] Divided 4374.32 4126.96 1.05994
1966 kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145] Subtracted 4619.81 4965.45 345.64
rd protein. [swissprot;acc:p18615] Divided 4374.32 4126.96 1.05994
1967 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 3678.56 3470.55
testis-specific bromodomain protein. [refseq;acc:nm_001726] Subtracted 5438.68 5783.2 344.52
1968 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Divided 4374.32 4126.96 1.05994
protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] Subtracted 5438.6 5783.11 344.51
1969 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Divided 4374.32 4126.96 1.05994
bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] Subtracted 5438.6 5783.11 344.51
1970 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Divided 4374.32 4126.96 1.05994
nag14 protein. [refseq;acc:nm_022143] Subtracted 5438.6 5783.11 344.51
1971 bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] 5438.52 5783.01 344.49
j domain containing protein 1. [swissprot;acc:q9ukb3] Divided 4374.32 4126.96 1.05994
1972 bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] Subtracted 5438.18 5782.62 344.44
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Divided 4374.32 4126.96 1.05994
1973 alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] Subtracted 7383.13 7727.39 344.26
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Divided 4374.32 4126.96 1.05994
1974 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 3678.62 3470.64 1.05993
lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [refseq;acc:nm_005358] Subtracted 5782.86 6126.69 343.83
1975 cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129] Divided 6988.29 7406.53 1.05985
ubiquitin. [swissprot;acc:p02248] Subtracted 7390.36 7733.85 343.49
1976 rho-gtpase-activating protein 8. [swissprot;acc:q9nsg0] 6036.68 6379.44 342.76
splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] Divided 5939.85 6294.91 1.05978
1977 lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [refseq;acc:nm_005358] 5782.86 6126.69 1.05946
rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [swissprot;acc:q07960] Subtracted 6036.68 6379.44 342.76
1978 kinesin light chain 2 (klc 2). [swissprot;acc:q9h0b6] 6036.62 6379.38
uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725] Divided 5475.74 5800.97 1.05939
1979 26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/