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 1823 to 1872 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
912 prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] Divided 4982.81 5480.91 1.09996
transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Subtracted 3847.31 4409.22 561.91
913 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] Divided 5768.5 6342.05 1.09943
914 cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] 6513.45 7161 1.09942
hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Subtracted 4997 5557.17 560.17
915 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Divided 6289.72 6911.96 1.09893
zinc finger protein t86. [swissprot;acc:o00488] Subtracted 4052.77 4612.54 559.77
916 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Divided 6289.72 6911.96 1.09893
pescadillo homolog 1. [swissprot;acc:o00541] Subtracted 3751.14 4310.89 559.75
917 nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Divided 6289.72 6911.96 1.09893
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Subtracted 5036.92 5596.36 559.44
918 scratch; scratch 1. [refseq;acc:nm_031309] Divided 7281.6 8001.64 1.09888
transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] Subtracted 6288.27 6846.97 558.7
919 limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Divided 5396.36 5929.41 1.09878
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Subtracted 6287.07 6845.28 558.21
920 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Divided 7273.78 7991.72 1.0987
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Subtracted 3761.59 4319.69 558.1
921 proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] 3831.17 4388.74 557.57
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Divided 6324.31 6948.5 1.0987
922 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Subtracted 3893.85 4450.98 557.13
tubulin-tyrosine ligase. [refseq;acc:nm_153712] Divided 5511.2 6054.71 1.09862
923 eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] 4057.54 4457.66 1.09861
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Subtracted 3790.11 4346.98 556.87
924 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] 10243.4 9686.82 556.58
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Divided 5406.5 5939.42 1.09857
925 grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] Subtracted 4134.77 4691.24 556.47
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Divided 5637.43 6193.07 1.09856
926 grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7] Subtracted 4134.77 4691.24 556.47
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Divided 5637.45 6193.08 1.09856
927 dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] 5638.64 6194.22 1.09853
swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077] Subtracted 4134.77 4691.24 556.47
928 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Divided 5638.46 6194.04 1.09853
swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078] Subtracted 4134.77 4691.24 556.47
929 surfeit locus protein 1. [swissprot;acc:q15526] Divided 5638.46 6194.04 1.09853
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] Subtracted 4134.77 4691.24 556.47
930 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Divided 5638.65 6194.23 1.09853
homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] Subtracted 6281.21 6837.61 556.4
931 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4]
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Divided 5638.59 6194.17 1.09853
932 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Subtracted 6281.21 6837.61 556.4
cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Divided 5638.46 6194.04 1.09853
933 cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Subtracted 6281.21 6837.61 556.4
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Divided 5638.46 6194.04 1.09853
934 hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] Subtracted 6281.21 6837.61 556.4
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] Divided 5640 6195.52 1.0985
935 homolog of yeast maf1. [refseq;acc:nm_032272] Subtracted 6133.83 6690.18 556.35
neurotrimin precursor (hnt). [swissprot;acc:q9p121] Divided 5413.63 5946.46 1.09842
936 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 5628.21 6180.37 1.09811
tumor differentially expressed protein 2. [refseq;acc:nm_178865] Subtracted 6133.83 6690.18 556.35

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/