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 25276 to 25325 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
2658 nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838] Ranked Subtracted 201.451 201.673 0.222
presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [swissprot;acc:p78352] Divided 216.933 216.7 1.00108
ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] Measured Subtracted 3640.58 3688.96 48.38
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] Rooted 72.1844 72.5201 0.3357
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Squared Divided 17922.9 17434.6 1.02801
2659 chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] Rooted 63.1205 63.4283 1.00488
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Subtracted 57.8738 58.2094 0.3356
mct-1 protein. [refseq;acc:nm_014060] Measured 4778.28 4732.13 46.15
nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [swissprot;acc:q15653] Ranked 201.452 201.674 0.222
nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838] Measured Divided 8277.7 8210.29 1.00821
presynaptic protein sap102 (synapse-associated protein 102) (neuroendocrine-dlg) (ne-dlg) (discs, large homolog 3). [swissprot;acc:q92796] Ranked 216.933 216.7 1.00108
zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] Squared 17924.3 17435.9 1.02801
zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] Subtracted 17957.5 17466.2 491.3
2660 kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9] Rooted Divided 63.1205 63.4283 1.00488
mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] Measured Subtracted 4778.28 4732.13 46.15
nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [swissprot;acc:q15653] Divided 8277.6 8210.21 1.00821
nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653] Ranked Subtracted 201.452 201.674 0.222
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Squared 36802.9 36313.4 489.5
peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044] Rooted 65.6325 65.3162 0.3163
presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959] Ranked Divided 216.937 216.704 1.00108
zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] Squared 17922.8 17434.6 1.028
2661 b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749] Ranked Subtracted 201.445 201.667 0.222
chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] Rooted 63.1205 63.4283 0.3078
conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746] Divided 1.00488
nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653] Measured 8277.66 8210.26 1.00821
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Ranked 204.768 204.549 1.00107
sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] Measured Subtracted 5327.58 5371.47 43.89
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Squared Divided 17920.4 17432.3 1.028
zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] Subtracted 17924.8 17436.3 488.5
2662 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] Measured 7780.98 7741.14 39.84
dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] Divided 4300.46 4334.66 1.00795
glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] Ranked Subtracted 214.575 214.354 0.221
kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9] Rooted 63.1205 63.4283 0.3078
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Divided 1.00488
molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] Ranked 204.768 204.549 1.00107
zinc finger protein 174 (aw-1). [swissprot;acc:q15697] Squared 17918.5 17430.6 1.02799
zinc finger protein 232. [swissprot;acc:q9uny5] Subtracted 17924 17435.6 488.4
2663 anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Ranked Divided 204.768 204.549 1.00107
conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746] Rooted Subtracted 63.1205 63.4283 0.3078
dynactin 4. [refseq;acc:nm_032486] Squared Divided 20932.4 20363.6 1.02793
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Measured 4608.54 4576.35 1.00703
peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044] Rooted 65.6325 65.3162 1.00484
similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6] Ranked Subtracted 216.288 216.067 0.221
sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864] Measured 7780.98 7741.14 39.84
zinc finger protein 99. [refseq;acc:nm_032164] Squared 17924.2 17435.8 488.4
2664 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] Ranked Divided 204.768 204.549 1.00107
ba207c16.2 (fragment). [sptrembl;acc:q9nql7] Squared 36982.9 35991.5 1.02755
bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Measured 4608.91 4576.78 1.00702
clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172] Subtracted 7780.98 7741.14 39.84
fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] Squared 36800.7 36312.3 488.4

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/