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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1851 to 1900 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
463 DDX18 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
POLR3F 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
464 AKT3 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
FNBP1 Ranked ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] 210.578 226.764 1.07686
HHEX Squared homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] 54726.7 45358.5 1.20654
RBBP7 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
465 AKT2 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
CHRNA7 Ranked neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 248.152 267.226 1.07686
E2F1 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
TRIT1 Squared trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] 25310.2 30537 1.20651
466 ADCY6 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
ATP2C2 Squared probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 25513.6 30779.5 1.2064
E2F2 Measured transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 3847.31 4409.22 1.14605
VAV3 Rooted vav-3 protein. [swissprot;acc:q9ukw4] 66.089 72.3555 1.09482
467 ADCY5 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
MTA1 Measured metastasis-associated protein mta1. [swissprot;acc:q13330] 4864.25 5573.62 1.14583
NUCB1 Squared nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] 23531.7 28371.6 1.20568
RPS5 Rooted 40s ribosomal protein s5. [swissprot;acc:p46782] 50.4649 46.1093 1.09446
468 CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 107.178 117.276 1.09422
LRRC15 Ranked leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] 248.152 267.226 1.07686
MLH1 Squared dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 23531.7 28371.6 1.20568
RBBP4 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
469 no value Rooted 60s ribosomal protein l9. [swissprot;acc:p32969] 51.1334 46.7335 1.09415
FEM1B 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
NOL1 Measured proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] 3831.17 4388.74 1.14554
NUCB2 Squared nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] 23531.7 28371.6 1.20568
470 BOP1 Measured block of proliferation 1. [swissprot;acc:q14137] 3796.24 4348.59 1.1455
LRRC3 Ranked leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] 248.152 267.226 1.07686
PPP2R1B 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
SNW1 Rooted nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] 60.0148 65.6429 1.09378
471 LAMC1 Ranked laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] 248.152 267.226 1.07686
MAPK11 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
PGK2 Squared phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] 28188.7 33982.7 1.20554
VAV2 Rooted vav-2 protein. [swissprot;acc:p52735] 66.088 72.2597 1.09339
472 ENO2 Squared gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] 28190.4 33984.1 1.20552
PUS1 Rooted trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] 50.3767 46.0753 1.09336
SLC46A2 Ranked thymic stromal co-transporter. [refseq;acc:nm_033051] 248.152 267.226 1.07686
SPHK1 Measured sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] 9649.61 11053.5 1.14549
473 DPAGT1 udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5]
ENO3 Squared beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] 28190.4 33984.1 1.20552
PRPF31 Ranked pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 225.661 209.651 1.07637
SEPHS2 Rooted selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 62.574 68.4128 1.09331
474 DLC1 Measured rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] 9649.61 11053.5 1.14549
ENO1 Squared alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] 28190.4 33984.1 1.20552
KCNA2 Ranked potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] 226.789 210.818 1.07576
MICAL2 Rooted flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] 62.574 68.4128 1.09331
475 INPP4B inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866]
KCNA1 Ranked potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] 226.727 210.816 1.07547
MAPKAPK2 Measured map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] 9649.61 11053.5 1.14549
PGK1 Squared phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] 28192 33985.3 1.20549

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
- Hugo is the HGNC identifier if it exists
- 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/