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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1812 to 1861 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
453 Rooted surfeit locus protein 5. [swissprot;acc:q15528] 50.4595 46.0413 1.09596
454 Measured guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] 3760.8 4315.06 1.14738
Ranked 40s ribosomal protein s26. [swissprot;acc:p02383] 210.224 226.578 1.07779
Squared sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] 31620.5 38250.7 1.20968
Rooted gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] 50.4595 46.0412 1.09596
455 Measured ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] 4890.51 5610.95 1.14731
Ranked mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] 210.225 226.578 1.07779
Squared 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
Rooted zinc finger protein 291. [swissprot;acc:q9by12] 50.4595 46.0413 1.09596
456 Measured 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] 4890.51 5610.95 1.14731
Ranked atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] 210.225 226.578 1.07779
Squared nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 10933.6 13219.6 1.20908
Rooted peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] 50.4595 46.0413 1.09596
457 Measured 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] 4890.51 5610.95 1.14731
Ranked ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] 210.225 226.578 1.07779
Squared nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 10936.1 13221.9 1.20901
Rooted protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] 50.4595 46.0413 1.09596
458 Measured elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 4890.55 5610.96 1.14731
Ranked signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 235.922 218.925 1.07764
Squared nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] 10950.4 13235.9 1.20871
Rooted 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] 50.2954 45.9216 1.09524
459 Measured myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] 4892.16 5611.48 1.14704
Ranked 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
Squared pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] 27096.7 32743.5 1.20839
Rooted vav proto-oncogene. [swissprot;acc:p15498] 66.0892 72.3741 1.0951
460 Measured nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] 3790.11 4346.98 1.14693
Ranked splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] 223.648 207.62 1.0772
Squared ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] 29547.4 35683.5 1.20767
Rooted protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] 50.6156 46.2239 1.09501
461 Measured grb2-related adaptor protein. [swissprot;acc:q13588] 5986.65 6865.68 1.14683
Ranked krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] 223.648 207.62 1.0772
Squared utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] 29544.1 35678.3 1.20763
Rooted 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 50.6156 46.2239 1.09501
462 Measured ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] 11383.2 9926.61 1.14674
Ranked mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] 254.434 236.224 1.07709
Squared 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] 29540.4 35672.6 1.20759
Rooted 40s ribosomal protein s3. [swissprot;acc:p23396] 50.6274 46.236 1.09498
463 Measured atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] 3720.18 4264.46 1.1463
Ranked dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] 238.921 257.327 1.07704
Squared calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] 25533.3 30810.8 1.20669
Rooted rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] 50.2317 55.0025 1.09498
464 Measured histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 4858.96 5568.85 1.1461
Ranked ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] 210.578 226.764 1.07686
Squared homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] 54726.7 45358.5 1.20654
Rooted rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] 50.2317 55.0025 1.09498
465 Measured 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] 3847.31 4409.22 1.14605
Ranked neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 248.152 267.226 1.07686
Squared trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] 25310.2 30537 1.20651
Rooted rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] 50.2317 55.0025 1.09498
466 Measured transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 3847.31 4409.22 1.14605

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/