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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
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 [...,...].
Value Type Network Comparison Type Gene Rank Interaction Map green description network_comparison red Filtered
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 77072 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
Interaction Map
green
description
network_comparison
red
918 High confidence 8001.64 scratch; scratch 1. [refseq;acc:nm_031309] 1.09888 7281.6
Low confidence 8609.86 nadp-dependent malic enzyme (ec 1.1.1.40) (nadp-me) (malic enzyme 1). [swissprot;acc:p48163] 1.03924 8284.79
919 High confidence 5929.41 limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] 1.09878 5396.36
Low confidence 7652.4 proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] 1.03922 7363.63
920 High confidence 7991.72 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 1.0987 7273.78
Low confidence 7652.73 proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] 1.03921 7363.99
921 High confidence 6948.5 translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] 1.0987 6324.31
Low confidence 7652.55 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] 1.03921 7363.79
922 High confidence 6054.71 tubulin-tyrosine ligase. [refseq;acc:nm_153712] 1.09862 5511.2
Low confidence 8300.91 xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] 1.03918 7987.95
923 High confidence 4457.66 eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] 1.09861 4057.54
Low confidence 8506.98 glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] 1.03915 8186.49
924 High confidence 5939.42 opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] 1.09857 5406.5
Low confidence 9404.18 syndecan-3 (synd3). [swissprot;acc:o75056] 1.03912 9050.12
925 High confidence 6193.07 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] 1.09856 5637.43
Low confidence 8726.39 my016 protein. [sptrembl;acc:q9h3k6] 1.03909 8398.07
926 High confidence 6193.08 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] 1.09856 5637.45
Low confidence 8366.23 tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 1.03905 8051.79
927 High confidence 6194.22 dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] 1.09853 5638.64
Low confidence 8318.27 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] 1.03902 8005.86
928 High confidence 6194.04 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] 1.09853 5638.46
Low confidence 8610.75 junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [swissprot;acc:q9y624] 1.03902 8287.37
929 High confidence 6194.04 surfeit locus protein 1. [swissprot;acc:q15526] 1.09853 5638.46
Low confidence 8385.43 citrate synthase, mitochondrial precursor (ec 2.3.3.1). [swissprot;acc:o75390] 1.03902 8070.54
930 High confidence 6194.23 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] 1.09853 5638.65
Low confidence 8237.48 elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] 1.039 7928.24
931 High confidence 6194.17 seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] 1.09853 5638.59
Low confidence 7935.35 acidic leucine-rich nuclear phosphoprotein 32 family member c (tumorigenic protein pp32r1). [swissprot;acc:o43423] 1.03899 7637.56
932 High confidence 6194.04 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] 1.09853 5638.46
Low confidence 7935.35 acidic leucine-rich nuclear phosphoprotein 32 family member a (potent heat-stable protein phosphatase 2a inhibitor i1pp2a) (hla-dr associated protein i) (phapi) (acidic nuclear phosphoprotein pp32) (cerebellar leucine rich acidic nuclear protein). [swissprot;acc:p39687] 1.03899 7637.56
933 High confidence 6194.04 protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] 1.09853 5638.46
Low confidence 7935.35 acidic leucine-rich nuclear phosphoprotein 32 family member d (tumorigenic protein pp32r2). [swissprot;acc:o95626] 1.03899 7637.56
934 High confidence 6195.52 [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] 1.0985 5640
Low confidence 7935.35 general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] 1.03899 7637.56
935 High confidence 5946.46 neurotrimin precursor (hnt). [swissprot;acc:q9p121] 1.09842 5413.63
Low confidence 7935.35 acidic leucine-rich nuclear phosphoprotein 32 family member b (phapi2 protein) (silver-stainable protein ssp29) (acidic protein rich in leucines). [swissprot;acc:q92688] 1.03899 7637.56
936 High confidence 6180.37 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 1.09811 5628.21
Low confidence 7935.35 bromodomain containing 8; thyroid hormone receptor coactivating protein; skeletal muscle abundant protein. [refseq;acc:nm_006696] 1.03899 7637.56
937 High confidence 6432.03 nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] 1.09776 5859.25
Low confidence 8534.22 protein x 0001. [refseq;acc:nm_016302] 1.03895 8214.28
938 High confidence 6432.03 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 1.09776 5859.25
Low confidence 8053.37 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] 1.03891 7751.77
939 High confidence 6432.03 nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] 1.09776 5859.25
Low confidence 8783.33 mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] 1.0389 8454.45
940 High confidence 6113.35 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] 1.09775 5568.96
Low confidence 7863.85 nocturnin (ccr4 protein homolog). [swissprot;acc:q9uk39] 1.0389 7569.42
941 High confidence 5455.34 caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] 1.09761 4970.21
Low confidence 8332.09 transcription factor ap-2 alpha (ap2-alpha) (activating enhancer- binding protein 2 alpha) (ap-2 transcription factor) (activator protein-2) (ap-2). [swissprot;acc:p05549] 1.0389 8020.09
942 High confidence 7240.64 phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] 1.09747 6597.56
Low confidence 8783.33 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 1.0389 8454.45

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/