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 1775 to 1824 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
888 lbp-9. [refseq;acc:nm_014553] Divided 5903.18 6506.32 1.10217
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
nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Subtracted 5859.25 6432.03 572.78
901 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 6080.91 6653.52 572.61
histone deacetylase 1 (hd1). [swissprot;acc:q13547] Divided 5929.61 6531.55 1.10151
902 estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] 10246.1 11285.8 1.10147
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Subtracted 3729.02 4301.58 572.56
903 fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] 6077.65 6649.22 571.57
red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] Divided 4986.58 5492.51 1.10146
904 exocyst complex component sec15b. [swissprot;acc:q9y2d4] Subtracted 6213.51 6785.04 571.53
importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Divided 6167.33 6785.98 1.10031
905 ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Subtracted 5168.43 4597.44 570.99
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] Divided 10230.1 11256.2 1.1003
906 ran-gtp binding protein (fragment). [sptrembl;acc:o60518] 6165.1 6783.01 1.10023
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Subtracted 5168.43 4597.44 570.99
907 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Divided 11852.9 10773.5 1.10019
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Subtracted 3779.92 4348.48 568.56
908 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Divided 11848.8 10770.3 1.10014
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Subtracted 3721.19 4288.17 566.98
909 kinesin family member c3. [refseq;acc:nm_005550] Divided 5995.49 6595.35 1.10005
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Subtracted 3758.67 4322.87 564.2
910 nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] 3766.03 4329.37 563.34
sipl protein. [refseq;acc:nm_018269] Divided 6522.94 7175.18 1.09999
911 ad24 protein. [refseq;acc:nm_022451] Subtracted 3753.71 4315.95 562.24
prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] Divided 4982.81 5480.91 1.09996
912 prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]
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

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/