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.


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 2080 to 2129 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
130 udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133] Rooted Subtracted 0 32.4121 28.377 4.0351
131 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Squared 101.05 1034.13 933.08
60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] Rooted Divided 19.3128 16.0484 1.20341
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Ranked 8375.43 9873.58 1.17887
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Subtracted 1 242.718 276.018 33.3
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Measured Divided 2234.73 2978.57 1.33285
glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075] Rooted Subtracted 0 32.4121 28.377 4.0351
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Divided 1 55.1113 67.5537 1.22577
integral membrane protein cii-3b. [sptrembl;acc:o75609] Ranked Subtracted 0 14951.6 13204.2 1747.4
nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Squared Divided 1 148058 99628.4 1.4861
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Measured Subtracted 0 4912.01 4658.69 253.32
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Rooted 1 144.606 157.824 13.218
serpin b11. [swissprot;acc:q96p15] Measured Divided 0 42 56 1.33333
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Ranked 1 294.053 242.562 1.21228
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Squared Subtracted 71062.4 95488.9 24426.5
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Measured 12839 10911.1 1927.9
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Squared Divided 0 451.156 817.981 1.81308
132 arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] Subtracted 5671.94 6590.82 918.88
autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] Divided 1 36359.2 24466.8 1.48606
creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Rooted 0 23.9003 19.8655 1.20311
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Measured 42 56 1.33333
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Ranked Subtracted 1 229.406 196.695 32.711
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Measured Divided 2236.61 2980.35 1.33253
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Rooted 44.963 55.0576 1.22451
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Squared 0 1.75053 0.969467 1.80566
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Ranked Subtracted 10883 12622.8 1739.8
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Squared 1 71062.2 95488.6 24426.4
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Rooted 144.606 157.824 13.218
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Ranked Divided 0 19048 22389 1.1754
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 1 350 290 1.2069
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Measured Subtracted 12839 10911.1 1927.9
udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537] Rooted 0 32.4121 28.377 4.0351
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Measured 1949.36 2202 252.64
133 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] Ranked Divided 6814 8009 1.17537
anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Rooted Subtracted 1 144.606 157.824 13.218
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Measured Divided 0 252 335 1.32937
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Subtracted 1 12798.9 10887.2 1911.7
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Ranked 226.887 194.72 32.167
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Measured Divided 23421.5 17580.4 1.33225
gbp protein isoform a. [refseq;acc:nm_017870] Squared 1182.25 1726.55 1.46039
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Subtracted 0 4748.4 5654.56 906.16
metaxin 1. [swissprot;acc:q13505] Divided 6149.89 3429.64 1.79316
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] Ranked Subtracted 17144.8 15405.6 1739.2
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Rooted Divided 1 45.4558 55.5995 1.22316
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Measured Subtracted 0 3036.85 2784.59 252.26
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Rooted Divided 27.4578 22.8323 1.20259
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Squared Subtracted 1 71062.2 95488.6 24426.4
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Ranked Divided 350 290 1.2069
udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855] Rooted Subtracted 0 32.4121 28.377 4.0351
134 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] Squared 3438.01 4339.96 901.95

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/