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 red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
network_comparison
green
795 serpin b11. [swissprot;acc:q96p15] Ranked 224.244 1.04578 234.511
796 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Measured 6834.54 1.11061 7590.49
placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] Ranked 224.244 1.04578 234.511
set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] Rooted 54.765 1.06481 51.4319
xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] Squared 25842.1 1.16451 30093.4
797 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Ranked 224.244 1.04578 234.511
importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] Measured 6834.54 1.11061 7590.49
limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Squared 22535.2 1.16433 26238.4
structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] Rooted 54.1622 1.06481 57.6725
798 cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] 54.765 51.4319
leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] Ranked 224.244 1.04578 234.511
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Squared 22587.2 1.1642 26296.1
transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Measured 6834.54 1.11061 7590.49
799 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Rooted 54.765 1.06481 51.4319
neurotrimin precursor (hnt). [swissprot;acc:q9p121] Squared 22623.7 1.16412 26336.8
sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] Ranked 221.965 1.04501 212.404
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Measured 6834.54 1.11061 7590.49
800 chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Rooted 54.1622 1.06481 57.6725
nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] Ranked 221.965 1.04501 212.404
orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] Measured 6075.55 1.1105 6746.92
phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] Squared 22210.6 1.1634 25839.9
801 beta-catenin (pro2286). [swissprot;acc:p35222] Ranked 224.445 1.04445 214.894
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] Rooted 54.765 1.06481 51.4319
importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] Measured 6456.35 1.1105 7169.75
phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Squared 22208.7 1.16322 25833.6
802 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 20131.3 1.16319 23416.5
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Measured 6455.66 1.11047 7168.82
testis-specific protein tex28. [swissprot;acc:o15482] Ranked 212.386 1.04425 221.785
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Rooted 54.6759 1.06474 51.3516
803 bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] Squared 22573.3 1.16308 26254.5
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Measured 6455.02 1.11045 7167.96
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] Ranked 212.386 1.04425 221.785
tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] Rooted 54.6759 1.06474 51.3516
804 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 74.3877 1.0646 79.1931
a kindred of iglon. [refseq;acc:nm_173808] Ranked 212.386 1.04425 221.785
nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Measured 6770.78 1.11036 7517.97
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Squared 24954.5 1.16302 29022.6
805 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Rooted 74.3557 1.0645 79.1513
60s ribosomal protein l39. [swissprot;acc:p02404] Measured 4708.61 1.11003 5226.71
ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] Ranked 212.386 1.04425 221.785
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Squared 15384.8 1.16284 17890
806 40s ribosomal protein s26. [swissprot;acc:p02383] Rooted 62.4161 1.06435 58.6426
60s ribosomal protein l18a. [swissprot;acc:q02543] Measured 4708.61 1.11003 5226.71
inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Ranked 212.386 1.04425 221.785
inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] Squared 25555.4 1.16278 29715.4
807 40s ribosomal protein s19. [swissprot;acc:p39019] Measured 4708.61 1.11003 5226.71
inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732] Squared 25560.1 1.16277 29720.6
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Rooted 62.416 1.06435 58.6426
palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Ranked 212.386 1.04425 221.785
808 60s ribosomal protein l31. [swissprot;acc:p12947] Measured 4708.61 1.11003 5226.71

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/