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 1836 to 1885 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
459 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
Ranked adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] 248.152 267.226 1.07686
Squared probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 25513.6 30779.5 1.2064
Rooted vav-3 protein. [swissprot;acc:q9ukw4] 66.089 72.3555 1.09482
467 Measured metastasis-associated protein mta1. [swissprot;acc:q13330] 4864.25 5573.62 1.14583
Ranked adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] 248.152 267.226 1.07686
Squared nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] 23531.7 28371.6 1.20568
Rooted 40s ribosomal protein s5. [swissprot;acc:p46782] 50.4649 46.1093 1.09446
468 Measured 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] 4869.15 5578.02 1.14558
Ranked leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] 248.152 267.226 1.07686
Squared dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 23531.7 28371.6 1.20568
Rooted t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 107.178 117.276 1.09422
469 Measured proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] 3831.17 4388.74 1.14554
Ranked fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] 248.152 267.226 1.07686
Squared nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] 23531.7 28371.6 1.20568
Rooted 60s ribosomal protein l9. [swissprot;acc:p32969] 51.1334 46.7335 1.09415
470 Measured block of proliferation 1. [swissprot;acc:q14137] 3796.24 4348.59 1.1455
Ranked leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] 248.152 267.226 1.07686
Squared serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] 10418.3 8641.84 1.20557
Rooted nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] 60.0148 65.6429 1.09378
471 Measured mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] 9649.61 11053.5 1.14549
Ranked laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] 248.152 267.226 1.07686
Squared phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] 28188.7 33982.7 1.20554
Rooted vav-2 protein. [swissprot;acc:p52735] 66.088 72.2597 1.09339
472 Measured sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] 9649.61 11053.5 1.14549

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/