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 6908 to 6957 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
432 mct-1 protein. [refseq;acc:nm_014060] Ranked Subtracted 1 226.313 243.03 16.717
mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Measured Divided 5244.71 6036.27 1.15093
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Subtracted 6739.81 7644.62 904.81
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Rooted 0 11.9476 12.4394 0.4918
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] Divided 12.5074 12.1701 1.02772
433 bystin. [swissprot;acc:q13895] Subtracted 29.2217 28.7356 0.4861
cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Squared 1 26598.9 32283.5 5684.6
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 0 2.36686 4.90793 2.54107
gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Measured 1 6739.82 7644.62 904.8
gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Rooted 66.082 71.6526 5.5706
grancalcin. [swissprot;acc:p28676] Squared Divided 29095.7 35338.3 1.21455
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Measured Subtracted 0 377.445 359.98 17.465
h2a histone family, member j isoform 1. [refseq;acc:nm_018267] Ranked 21205 20914 291
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Rooted Divided 1 54.4927 49.6125 1.09837
mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Measured 5244.88 6036.38 1.15091
mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] Ranked Subtracted 226.313 243.03 16.717
my016 protein. [sptrembl;acc:q9h3k6] Squared Divided 0 1279.28 1234.42 1.03634
programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] Ranked 1 212.547 229.411 1.07934
rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] Rooted 0 13.7373 13.373 1.02724
sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3] Measured 100.5 103.25 1.02736
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Ranked 772 754 1.02387
434 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] Measured Subtracted 2281.12 2263.85 17.27
ad24 protein. [refseq;acc:nm_022451] Ranked 1 251.334 234.672 16.662
cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] Rooted Divided 0 14.6265 15.0206 1.02694
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Subtracted 55.5596 55.0873 0.4723
elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] Ranked Divided 10028.5 10261.5 1.02323
gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Measured Subtracted 1 6739.83 7644.63 904.8
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Rooted 66.082 71.6526 5.5706
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Squared 26598.9 32283.5 5684.6
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Ranked 0 12532.2 12808.8 276.6
small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678] Squared 8.27667 5.86733 2.40934
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Divided 1 18306.1 22230.6 1.21438
t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] Ranked 212.547 229.411 1.07934
testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] Measured 0 201 206.5 1.02736
thymic stromal co-transporter. [refseq;acc:nm_033051] Rooted 1 54.4927 49.6125 1.09837
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Measured 5246.38 6037.37 1.15077
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Squared 0 3778.25 3909.18 1.03465
435 60s ribosomal protein l19. [swissprot;acc:p14118] Rooted 1 50.832 46.3081 1.09769
alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] Measured Subtracted 0 2319.24 2335.98 16.74
cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] Ranked 14010.2 13737.2 273
cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Squared Divided 1 26598.9 32283.5 1.21372
elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] Measured 0 5891.28 5737.71 1.02677
enigma protein; lim domain protein. [refseq;acc:nm_005451] Squared Subtracted 21.836 19.5177 2.3183
gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Measured 1 6739.82 7644.62 904.8
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Ranked Divided 0 8770.94 8574.04 1.02296
neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] Rooted 14.6265 15.0206 1.02694
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Subtracted 1 66.082 71.6526 5.5706
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Ranked Divided 221.522 205.286 1.07909
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Measured 5233.86 6022.6 1.1507
seven in absentia homolog 1. [refseq;acc:nm_003031] Rooted Subtracted 0 28.462 28.9328 0.4708

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/