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 1800 to 1849 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
900 dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] Low confidence 7782.19 8091.07 1.03969
901 histone deacetylase 1 (hd1). [swissprot;acc:q13547] High confidence 5929.61 6531.55 1.10151
nad-dependent malic enzyme, mitochondrial precursor (ec 1.1.1.38) (nad-me) (malic enzyme 2). [swissprot;acc:p23368] Low confidence 8286.72 8615.62 1.03969
902 estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] High confidence 10246.1 11285.8 1.10147
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Low confidence 7793.77 8102.84 1.03966
903 dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4]
red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] High confidence 4986.58 5492.51 1.10146
904 importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] 6167.33 6785.98 1.10031
mitochondrial ribosomal protein l44. [refseq;acc:nm_022915] Low confidence 7249.49 7536.94 1.03965
905 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 8037.95 8356.41 1.03962
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] High confidence 10230.1 11256.2 1.1003
906 cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Low confidence 8118 8439.57 1.03961
ran-gtp binding protein (fragment). [sptrembl;acc:o60518] High confidence 6165.1 6783.01 1.10023
907 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 11852.9 10773.5 1.10019
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Low confidence 8269.76 8597.34 1.03961
908 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] High confidence 11848.8 10770.3 1.10014
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] Low confidence 7589.77 7890.14 1.03958
909 kinesin family member c3. [refseq;acc:nm_005550] High confidence 5995.49 6595.35 1.10005
lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] Low confidence 8334.78 8664.4 1.03955
910 ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 8038.63 8356.55
sipl protein. [refseq;acc:nm_018269] High confidence 6522.94 7175.18 1.09999
911 phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Low confidence 8377.49 8708.47 1.03951
prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] High confidence 4982.81 5480.91 1.09996
912 monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283] Low confidence 8251.26 8577.2 1.0395
prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] High confidence 4982.81 5480.91 1.09996
913 nadp-dependent malic enzyme, mitochondrial precursor (ec 1.1.1.40) (nadp-me) (malic enzyme 3). [swissprot;acc:q16798] Low confidence 8275.91 8602.07 1.03941
ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] High confidence 5768.5 6342.05 1.09943
914 cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] 6513.45 7161 1.09942
integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] Low confidence 7948.13 8260.82 1.03934
915 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] High confidence 6289.72 6911.96 1.09893
integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Low confidence 7948.13 8260.82 1.03934
916 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] High confidence 6289.72 6911.96 1.09893
integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Low confidence 7948.13 8260.82 1.03934
917 26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556] 8126.23 8445.39 1.03928
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] High confidence 6289.72 6911.96 1.09893
918 nadp-dependent malic enzyme (ec 1.1.1.40) (nadp-me) (malic enzyme 1). [swissprot;acc:p48163] Low confidence 8284.79 8609.86 1.03924
scratch; scratch 1. [refseq;acc:nm_031309] High confidence 7281.6 8001.64 1.09888
919 limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] 5396.36 5929.41 1.09878
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Low confidence 7363.63 7652.4 1.03922
920 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] High confidence 7273.78 7991.72 1.0987
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Low confidence 7363.99 7652.73 1.03921
921 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] 7363.79 7652.55
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] High confidence 6324.31 6948.5 1.0987
922 tubulin-tyrosine ligase. [refseq;acc:nm_153712] 5511.2 6054.71 1.09862
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Low confidence 7987.95 8300.91 1.03918
923 eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] High confidence 4057.54 4457.66 1.09861
glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] Low confidence 8186.49 8506.98 1.03915
924 opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] High confidence 5406.5 5939.42 1.09857
syndecan-3 (synd3). [swissprot;acc:o75056] Low confidence 9050.12 9404.18 1.03912
925 my016 protein. [sptrembl;acc:q9h3k6] 8398.07 8726.39 1.03909

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/