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.


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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 3008 to 3057 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
376 utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Squared Subtracted 29544.1 35678.3 6134.2
377 dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] Ranked Divided 242.691 265.481 1.09391
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Measured Subtracted 4252.66 5213.05 960.39
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Ranked 248.152 267.226 19.074
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Rooted Divided 50.2554 45.5687 1.10285
nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Measured 17385.9 14889.2 1.16769
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Squared 33044.9 40781.4 1.23412
serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Rooted Subtracted 61.2684 67.755 6.4866
ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] Squared 29540.4 35672.6 6132.2
378 60s ribosomal protein l30. [swissprot;acc:p04645] Ranked Divided 242.593 265.365 1.09387
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Squared 15034.5 18552.2 1.23398
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Ranked Subtracted 248.152 267.226 19.074
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Measured Divided 12471.7 14561.7 1.16758
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Rooted 50.5816 45.8738 1.10263
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Squared Subtracted 30286.5 36362 6075.5
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Rooted 47.3621 53.8355 6.4734
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Measured 6272.91 7226.06 953.15
379 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] Ranked Divided 241.509 264.163 1.0938
aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Squared 33010.8 40732.2 1.23391
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Ranked Subtracted 248.152 267.226 19.074
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Rooted Divided 59.5128 65.604 1.10235
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Measured 6704.44 7811.45 1.16512
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Subtracted 4244.95 5193.42 948.47
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Rooted 86.5959 93.0684 6.4725
tubby protein homolog. [swissprot;acc:p50607] Squared 30286.5 36362 6075.5
380 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Measured Divided 12998.5 15138.2 1.16461
calcyphosine. [swissprot;acc:q13938] Rooted 59.5128 65.604 1.10235
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Ranked Subtracted 248.152 267.226 19.074
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Measured 4641.09 5588.75 947.66
ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Squared Divided 32991.5 40704.5 1.23379
protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Subtracted 30286.5 36362 6075.5
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Ranked Divided 242.109 264.79 1.09368
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Rooted Subtracted 96.6463 103.103 6.4567
381 c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 86.4264 92.8635 6.4371
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Divided 59.5128 65.604 1.10235
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Measured 5246.01 6109.31 1.16456
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Subtracted 4641.09 5588.75 947.66
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Squared 30286.5 36362 6075.5
ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Divided 32987.4 40698.5 1.23376
thymic stromal co-transporter. [refseq;acc:nm_033051] Ranked Subtracted 248.152 267.226 19.074
transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Divided 200.586 183.423 1.09357
382 40s ribosomal protein s23. [swissprot;acc:p39028] Rooted 49.8325 45.2077 1.1023
atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Ranked Subtracted 253.852 234.808 19.044
cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Rooted 66.4284 60.0004 6.428
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Measured Divided 4533.74 5279.4 1.16447
rna-binding protein. [refseq;acc:nm_019027] Squared 15043.7 18560.1 1.23375
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Measured Subtracted 2397.19 3343.62 946.43
tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Ranked Divided 200.791 183.66 1.09328
tbc1 domain family member 5. [swissprot;acc:q92609] Squared Subtracted 30286.5 36362 6075.5
383 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Rooted Divided 49.8325 45.2077 1.1023

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/