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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Gene Rank description Network Comparison Type Value Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 3630 to 3679 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
Value Type
red
green
network_comparison
454 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Divided Rooted 50.4595 46.0412 1.09596
guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Measured 3760.8 4315.06 1.14738
sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] Squared 31620.5 38250.7 1.20968
455 acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] 31597.8 38216.9 1.20948
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Subtracted Ranked 224.161 207.972 16.189
cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Rooted 61.1902 66.6503 5.4601
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Measured 398.5 1281.5 883
ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Divided 4890.51 5610.95 1.14731
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Ranked 210.225 226.578 1.07779
nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838] Subtracted Squared 50588.2 45100.2 5488
zinc finger protein 291. [swissprot;acc:q9by12] Divided Rooted 50.4595 46.0413 1.09596
456 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] Ranked 210.225 226.578 1.07779
ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Measured 4890.51 5610.95 1.14731
nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653] Subtracted Squared 50587.8 45099.9 5487.9
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Divided 10933.6 13219.6 1.20908
peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Rooted 50.4595 46.0413 1.09596
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Subtracted Measured 398.5 1281.5 883
transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Rooted 72.9862 78.4342 5.448
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Ranked 224.161 207.972 16.189
457 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] 210.578 226.764 16.186
nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Divided Measured 4890.51 5610.95 1.14731
nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [swissprot;acc:q15653] Subtracted Squared 50587.2 45099.6 5487.6
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Divided 10936.1 13221.9 1.20901
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Rooted 50.4595 46.0413 1.09596
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] Subtracted 72.8809 78.3254 5.4445
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Measured 4620.76 5501.94 881.18
ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] Divided Ranked 210.225 226.578 1.07779
458 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Rooted 50.2954 45.9216 1.09524
atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Subtracted Ranked 251.653 235.506 16.147
elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Divided Measured 4890.55 5610.96 1.14731
grb2-related adaptor protein. [swissprot;acc:q13588] Subtracted 5986.65 6865.68 879.03
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Divided Squared 10950.4 13235.9 1.20871
phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903] Subtracted 26874.6 32347.4 5472.8
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Rooted 49.0663 54.4978 5.4315
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Divided Ranked 235.922 218.925 1.07764
459 bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] 233.529 216.737 1.07748
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Measured 4892.16 5611.48 1.14704
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Subtracted Rooted 55.1073 60.5285 5.4212
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Ranked 250.538 234.401 16.137
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Divided Squared 27096.7 32743.5 1.20839
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Subtracted Measured 5082.66 5959.99 877.33
solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] Squared 26867.3 32335.2 5467.9
vav proto-oncogene. [swissprot;acc:p15498] Divided Rooted 66.0892 72.3741 1.0951
460 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Subtracted Measured 1931.34 1057.39 873.95
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Divided 3790.11 4346.98 1.14693
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Rooted 50.6156 46.2239 1.09501
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Subtracted 98.7609 93.3602 5.4007
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Ranked 186.52 170.42 16.1
solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183] Squared 26867.3 32335.2 5467.9
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Divided Ranked 223.648 207.62 1.0772

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/