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.


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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1750 to 1799 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
875 steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Divided 10263.8 11318.6 1.10277
876 peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] 5644.68 6223.23 1.10249
ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] Subtracted 9946.21 9367.66 578.55
877 mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Divided 5797.88 6391.75 1.10243
peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Subtracted 5644.68 6223.23 578.55
878 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Divided 5797.88 6391.75 1.10243
sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Subtracted 6600.36 7178.84 578.48
879 nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Divided 5797.88 6391.75 1.10243
ran binding protein 11. [refseq;acc:nm_016338] Subtracted 6138.91 6717.05 578.14
880 membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] 6136.99 6714.98 577.99
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Divided 5166.04 5694.55 1.1023
881 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 5912.84 6517.69 1.10229
neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] Subtracted 5595.65 6173.23 577.58
882 ring finger protein 44. [refseq;acc:nm_014901]
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] Divided 5912.84 6517.69 1.10229
883 adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]
phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] Subtracted 5595.65 6173.23 577.58
884 mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Divided 5167.15 5695.44 1.10224
ring finger protein 38. [refseq;acc:nm_022781] Subtracted 5595.65 6173.23 577.58
885 mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] Divided 5168.01 5696.12 1.10219
phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] Subtracted 5595.65 6173.23 577.58
886 sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770]
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Divided 5903.18 6506.32 1.10217
887 atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] Subtracted 5595.65 6173.23 577.58
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Divided 5903.18 6506.32 1.10217
888 lbp-9. [refseq;acc:nm_014553]
phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] Subtracted 5595.65 6173.23 577.58
889 s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] 6123.15 6700.05 576.9
splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] Divided 5903.18 6506.32 1.10217
890 mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Subtracted 3594.31 4169.95 575.64
tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] Divided 5350.87 5896.82 1.10203
891 lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] 5385.04 5933.65 1.10188
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Subtracted 3804.09 4379.37 575.28
892 cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Divided 6784.67 7475.48 1.10182
mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] Subtracted 6599.84 7174.29 574.45
893 e-1 enzyme. [refseq;acc:nm_021204] Divided 6603.09 7274.72 1.10171
probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] Subtracted 6599.84 7174.29 574.45
894 parafibromin. [refseq;acc:nm_024529] Divided 4331.17 4771.22 1.1016
tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226] Subtracted 6599.84 7174.29 574.45
895 heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Divided 10247.8 11289 1.1016
ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] Subtracted 5768.5 6342.05 573.55
896 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 5167.88 4594.43 573.45
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Divided 5208.27 5737.17 1.10155
897 exocyst complex component sec15a. [swissprot;acc:q8tag9] Subtracted 6201.54 6774.35 572.81
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Divided 5929.48 6531.48 1.10153
898 multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] 5929.55 6531.52 1.10152
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] Subtracted 5859.25 6432.03 572.78
899 dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Divided 5929.55 6531.52 1.10152
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Subtracted 5859.25 6432.03 572.78
900 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Divided 4713.58 4279.17 1.10152

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/