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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2130 to 2179 of 77072 in total
Rank
description
Value Type
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
67 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Rooted Subtracted High confidence 0 7.90063 14.4058 6.50517
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] Ranked Divided 10793.5 14291.5 1.32408
protein kinase, lysine deficient 3. [refseq;acc:nm_020922] Subtracted Low confidence 13320.5 10324.5 2996
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Measured High confidence 4755.32 4320.09 435.23
Ranked 8932.56 11823.3 2890.74
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Low confidence 1 195.817 215.516 19.699
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Measured High confidence 17756.5 14007.3 3749.2
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Ranked Divided Low confidence 165.535 149.799 1.10505
septin 6. [swissprot;acc:q14141] Squared 74378.4 93531.9 1.25751
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Ranked Subtracted High confidence 187.458 243.677 56.219
similar to zinc finger protein 20 (zinc finger protein kox13) (dkfzp572p0920). [refseq;acc:nm_145233] Measured Low confidence 0 2354.39 1971.25 383.14
solute carrier family 2, facilitated glucose transporter, member 11 (glucose transporter type 11) (glucose transporter type 10). [swissprot;acc:q9byw1] Squared 17680 21426.5 3746.5
tenascin-x precursor (tn-x) (hexabrachion-like). [swissprot;acc:p22105] Rooted 16.4556 21.1366 4.681
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Squared Divided 50.8715 15.2519 3.33542
udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] Subtracted High confidence 6123.28 3763.18 2360.1
68 40s ribosomal protein s26. [swissprot;acc:p02383] Ranked 14269.7 17098 2828.3
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] Squared Divided Low confidence 50.642 15.1833 3.33538
60s ribosomal protein l37a. [swissprot;acc:p12751] Ranked 1 239.692 217.005 1.10455
Rooted Subtracted 57.2649 64.3669 7.102
alpha crystallin a chain. [swissprot;acc:p02489] Divided High confidence 0 6.22183 8.63381 1.38766
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Measured 1 6475.5 10307.5 1.59177
cyclin g2. [swissprot;acc:q16589] Subtracted 17738.6 13995.7 3742.9
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 0 6452.66 6019.79 432.87
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Ranked Low confidence 9449.27 12378.5 2929.23
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Squared High confidence 1 139741 78454.6 61286.4
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Rooted Low confidence 0 14.2989 18.9308 4.6319
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] High confidence 1 63.8686 47.2654 16.6032
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided 1.35128
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Ranked 267.139 336.075 1.25805
hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096] Rooted Low confidence 0 18.3618 12.9627 1.41651
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Squared High confidence 1 219048 129762 1.68808
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 31.36 0.00001 3136000
nadh-ubiquinone oxidoreductase mlrq subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-mlrq) (ci-mlrq). [swissprot;acc:o00483] Measured Low confidence 394 734 1.86294
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Squared Subtracted 1 52168.6 64594.5 12425.9
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Rooted High confidence 0 93.6109 87.2238 6.3871
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Ranked Low confidence 1 225.735 245.308 19.573
protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] Measured Divided High confidence 0 198.964 351.772 1.76802
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Ranked 8932.56 11823.3 1.32362
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Measured Low confidence 1 19498.1 17265.4 1.12932
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Rooted 55.9786 61.8641 1.10514
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Ranked 0 7803.58 9824.6 1.25899
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Squared 1 27909.1 35068.7 1.25653
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Ranked Subtracted High confidence 187.462 243.673 56.211
solute carrier family 2, facilitated glucose transporter, member 5 (glucose transporter type 5, small intestine) (fructose transporter). [swissprot;acc:p22732] Squared Low confidence 0 17657.7 21397.2 3739.5
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Measured 1 1972.65 2998.1 1025.45
udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310] Squared High confidence 0 6123.28 3763.18 2360.1
zinc finger protein 222. [swissprot;acc:q9uk12] Measured Low confidence 2354.39 1971.25 383.14
69 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Rooted High confidence 11.844 18.0183 6.1743
a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Squared Low confidence 1 63411.7 51068.8 12342.9
amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] Measured Divided 6991.78 7848.45 1.12253

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/