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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1862 to 1911 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
466 ATP2C2 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Squared 25513.6 30779.5 1.2064
E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Measured 3847.31 4409.22 1.14605
VAV3 vav-3 protein. [swissprot;acc:q9ukw4] Rooted 66.089 72.3555 1.09482
467 ADCY5 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
MTA1 metastasis-associated protein mta1. [swissprot;acc:q13330] Measured 4864.25 5573.62 1.14583
NUCB1 nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] Squared 23531.7 28371.6 1.20568
RPS5 40s ribosomal protein s5. [swissprot;acc:p46782] Rooted 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 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Ranked 248.152 267.226 1.07686
MLH1 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Squared 23531.7 28371.6 1.20568
RBBP4 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
469 no value 60s ribosomal protein l9. [swissprot;acc:p32969] Rooted 51.1334 46.7335 1.09415
FEM1B 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
NOL1 proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Measured 3831.17 4388.74 1.14554
NUCB2 nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Squared 23531.7 28371.6 1.20568
470 BOP1 block of proliferation 1. [swissprot;acc:q14137] Measured 3796.24 4348.59 1.1455
LRRC3 leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Ranked 248.152 267.226 1.07686
PPP2R1B 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] Squared 10418.3 8641.84 1.20557
SNW1 nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Rooted 60.0148 65.6429 1.09378
471 LAMC1 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Ranked 248.152 267.226 1.07686
MAPK11 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] Measured 9649.61 11053.5 1.14549
PGK2 phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Squared 28188.7 33982.7 1.20554
VAV2 vav-2 protein. [swissprot;acc:p52735] Rooted 66.088 72.2597 1.09339
472 ENO2 gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Squared 28190.4 33984.1 1.20552
PUS1 trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Rooted 50.3767 46.0753 1.09336
SLC46A2 thymic stromal co-transporter. [refseq;acc:nm_033051] Ranked 248.152 267.226 1.07686
SPHK1 sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Measured 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 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Squared 28190.4 33984.1 1.20552
PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Ranked 225.661 209.651 1.07637
SEPHS2 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Rooted 62.574 68.4128 1.09331
474 DLC1 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] Measured 9649.61 11053.5 1.14549
ENO1 alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] Squared 28190.4 33984.1 1.20552
KCNA2 potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] Ranked 226.789 210.818 1.07576
MICAL2 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Rooted 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 potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] Ranked 226.727 210.816 1.07547
MAPKAPK2 map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Measured 9649.61 11053.5 1.14549
PGK1 phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] Squared 28192 33985.3 1.20549
476 CHRNA6 neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Measured 9649.61 11053.5 1.14549
KCNA4 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] Ranked 226.681 210.814 1.07527
SEPHS1 selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Rooted 62.574 68.4128 1.09331
VAV1 vav proto-oncogene. [swissprot;acc:p15498] Squared 31223.8 37614.3 1.20467
477 INPP4A inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Rooted 62.574 68.4128 1.09331
ISCU nitrogen fixation cluster-like. [refseq;acc:nm_014301] Measured 9649.61 11053.5 1.14549
NIP7 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Ranked 251.926 234.547 1.0741
VAV3 vav-3 protein. [swissprot;acc:q9ukw4] Squared 31248.8 37623.4 1.204
478 BRF1 transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Ranked 228.051 212.321 1.07409
HIST1H2BL histone h2b.c (h2b/c). [swissprot;acc:q99880] Rooted 50.6084 55.2961 1.09263
SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Squared 16318.4 19645.8 1.2039

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/