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 1825 to 1874 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
457 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] Measured 4890.51 5610.95 1.14731
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Squared 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
ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] 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
elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Measured 4890.55 5610.96 1.14731
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Squared 10950.4 13235.9 1.20871
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 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
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Squared 27096.7 32743.5 1.20839
vav proto-oncogene. [swissprot;acc:p15498] Rooted 66.0892 72.3741 1.0951
460 nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Measured 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
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Ranked 223.648 207.62 1.0772
ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Squared 29547.4 35683.5 1.20767
461 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Rooted 50.6156 46.2239 1.09501
grb2-related adaptor protein. [swissprot;acc:q13588] Measured 5986.65 6865.68 1.14683
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] Ranked 223.648 207.62 1.0772
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Squared 29544.1 35678.3 1.20763
462 40s ribosomal protein s3. [swissprot;acc:p23396] Rooted 50.6274 46.236 1.09498
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Ranked 254.434 236.224 1.07709
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] Measured 11383.2 9926.61 1.14674
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 1.20759
463 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Measured 3720.18 4264.46 1.1463
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] Squared 25533.3 30810.8 1.20669
dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] Ranked 238.921 257.327 1.07704
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Rooted 50.2317 55.0025 1.09498
464 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] Ranked 210.578 226.764 1.07686
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Measured 4858.96 5568.85 1.1461
homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] Squared 54726.7 45358.5 1.20654
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] Rooted 50.2317 55.0025 1.09498
465 neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Ranked 248.152 267.226 1.07686
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] Rooted 50.2317 55.0025 1.09498
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] Measured 3847.31 4409.22 1.14605
trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Squared 25310.2 30537 1.20651
466 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Ranked 248.152 267.226 1.07686
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Squared 25513.6 30779.5 1.2064
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Measured 3847.31 4409.22 1.14605
vav-3 protein. [swissprot;acc:q9ukw4] Rooted 66.089 72.3555 1.09482
467 40s ribosomal protein s5. [swissprot;acc:p46782] 50.4649 46.1093 1.09446
adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Ranked 248.152 267.226 1.07686
metastasis-associated protein mta1. [swissprot;acc:q13330] Measured 4864.25 5573.62 1.14583
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] Squared 23531.7 28371.6 1.20568
468 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Measured 4869.15 5578.02 1.14558
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Squared 23531.7 28371.6 1.20568
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Ranked 248.152 267.226 1.07686
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Rooted 107.178 117.276 1.09422
469 60s ribosomal protein l9. [swissprot;acc:p32969] 51.1334 46.7335 1.09415
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Ranked 248.152 267.226 1.07686

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/