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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 1880 to 1929 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
470 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
476 CHRNA6 Measured neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] 9649.61 11053.5 1.14549
KCNA4 Ranked 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
SEPHS1 Rooted 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
VAV1 Squared vav proto-oncogene. [swissprot;acc:p15498] 31223.8 37614.3 1.20467
477 INPP4A Rooted 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
ISCU Measured nitrogen fixation cluster-like. [refseq;acc:nm_014301] 9649.61 11053.5 1.14549
NIP7 Ranked saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] 251.926 234.547 1.0741
VAV3 Squared vav-3 protein. [swissprot;acc:q9ukw4] 31248.8 37623.4 1.204
478 BRF1 Ranked 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
HIST1H2BL Rooted histone h2b.c (h2b/c). [swissprot;acc:q99880] 50.6084 55.2961 1.09263
SRP9 Squared signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 16318.4 19645.8 1.2039
STARD13 Measured star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] 9649.61 11053.5 1.14549
479 EIF5B Squared translation initiation factor if-2. [swissprot;acc:o60841] 24031.6 28929.7 1.20382
HIST2H2BA Rooted histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 50.6084 55.2961 1.09263
NOLA1 Ranked nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 228.051 212.321 1.07409
STARD8 Measured star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] 9649.61 11053.5 1.14549
480 no value Rooted 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
CDS1 Squared 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
CHRNA2 Measured neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] 9649.61 11053.5 1.14549
NETO2 Ranked neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] 237.109 254.667 1.07405
481 no value Rooted histone h2b. [refseq;acc:nm_175055] 50.6084 55.2961 1.09263
MAPKAPK3 Measured mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] 9649.61 11053.5 1.14549
NETO1 Ranked neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] 237.109 254.667 1.07405
SRP9 Squared signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 16335.9 19660.7 1.20353
482 no value Rooted histone h2b.s (h2b/s). [swissprot;acc:p57053] 50.6084 55.2961 1.09263
HNRNPU Ranked heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] 237.109 254.667 1.07405
MAPK14 Measured 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
SLC13A3 Squared 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
483 no value Rooted histone h2b.d (h2b/d). [swissprot;acc:q99877] 50.6084 55.2961 1.09263

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/