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 Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1880 to 1929 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
Hugo
description
red
green
network_comparison
470 Rooted SNW1 nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] 60.0148 65.6429 1.09378
471 Measured 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] 9649.61 11053.5 1.14549
Ranked LAMC1 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] 248.152 267.226 1.07686
Squared PGK2 phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] 28188.7 33982.7 1.20554
Rooted VAV2 vav-2 protein. [swissprot;acc:p52735] 66.088 72.2597 1.09339
472 Measured SPHK1 sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] 9649.61 11053.5 1.14549
Ranked SLC46A2 thymic stromal co-transporter. [refseq;acc:nm_033051] 248.152 267.226 1.07686
Squared ENO2 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
Rooted PUS1 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
473 Measured 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] 9649.61 11053.5 1.14549
Ranked PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 225.661 209.651 1.07637
Squared ENO3 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
Rooted SEPHS2 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 Measured 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] 9649.61 11053.5 1.14549
Ranked KCNA2 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
Squared 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] 28190.4 33984.1 1.20552
Rooted MICAL2 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] 62.574 68.4128 1.09331
475 Measured MAPKAPK2 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
Ranked KCNA1 potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] 226.727 210.816 1.07547
Squared PGK1 phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] 28192 33985.3 1.20549
Rooted INPP4B inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] 62.574 68.4128 1.09331
476 Measured CHRNA6 neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] 9649.61 11053.5 1.14549
Ranked KCNA4 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] 226.681 210.814 1.07527
Squared VAV1 vav proto-oncogene. [swissprot;acc:p15498] 31223.8 37614.3 1.20467
Rooted SEPHS1 selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] 62.574 68.4128 1.09331
477 Measured ISCU nitrogen fixation cluster-like. [refseq;acc:nm_014301] 9649.61 11053.5 1.14549
Ranked NIP7 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] 251.926 234.547 1.0741
Squared VAV3 vav-3 protein. [swissprot;acc:q9ukw4] 31248.8 37623.4 1.204
Rooted 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] 62.574 68.4128 1.09331
478 Measured STARD13 star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] 9649.61 11053.5 1.14549
Ranked 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] 228.051 212.321 1.07409
Squared SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 16318.4 19645.8 1.2039
Rooted HIST1H2BL histone h2b.c (h2b/c). [swissprot;acc:q99880] 50.6084 55.2961 1.09263
479 Measured STARD8 star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] 9649.61 11053.5 1.14549
Ranked NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 228.051 212.321 1.07409
Squared EIF5B translation initiation factor if-2. [swissprot;acc:o60841] 24031.6 28929.7 1.20382
Rooted HIST2H2BA histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 50.6084 55.2961 1.09263
480 Measured CHRNA2 neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] 9649.61 11053.5 1.14549
Ranked NETO2 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] 237.109 254.667 1.07405
Squared CDS1 phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903] 26874.6 32347.4 1.20364
Rooted no value histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] 50.6084 55.2961 1.09263
481 Measured MAPKAPK3 mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] 9649.61 11053.5 1.14549
Ranked NETO1 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] 237.109 254.667 1.07405
Squared SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 16335.9 19660.7 1.20353
Rooted no value histone h2b. [refseq;acc:nm_175055] 50.6084 55.2961 1.09263
482 Measured MAPK14 mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] 9649.61 11053.5 1.14549
Ranked HNRNPU heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] 237.109 254.667 1.07405
Squared SLC13A3 solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] 26867.3 32335.2 1.20352
Rooted no value histone h2b.s (h2b/s). [swissprot;acc:p57053] 50.6084 55.2961 1.09263
483 Measured CHRNA4 neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] 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
- 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/