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.


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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 1680 to 1729 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
840 poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Divided 5786.67 6395.78 1.10526
841 conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] Subtracted 10300 9701.33 598.67
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Divided 5786.67 6395.78 1.10526
842 atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705] Subtracted 5623.18 6218.77 595.59
loh1cr12. [refseq;acc:nm_058169] Divided 5195.48 5741.63 1.10512
843 28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2] Subtracted 5623.18 6218.77 595.59
unr protein. [swissprot;acc:o75534] Divided 5195.48 5741.63 1.10512
844 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Subtracted 3641.89 4236.95 595.06
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Divided 6276.97 6934.8 1.1048
845 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]
mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Subtracted 5797.88 6391.75 593.87
846 biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] Divided 5607.43 6194.98 1.10478
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Subtracted 5797.88 6391.75 593.87
847 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Divided 6776.85 7485.55 1.10458
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Subtracted 5797.88 6391.75 593.87
848 phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903] 6441.56 7034.86 593.3
wd-repeat protein bing4. [swissprot;acc:o15213] Divided 4066.56 4491.65 1.10453
849 dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] 6194.15 6839.37 1.10417
solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] Subtracted 6439.63 7032.19 592.56
850 propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] Divided 6194.15 6839.37 1.10417
solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] Subtracted 6439.66 7032.22 592.56
851 casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] Divided 4307.12 4755.03 1.10399
solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2] Subtracted 6439.63 7032.19 592.56
852 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] Divided 4307.12 4755.03 1.10399
solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183] Subtracted 6439.66 7032.22 592.56
853 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] Divided 4078.45 4502.32 1.10393
secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] Subtracted 6439.35 7031.8 592.45
854 secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] 6439.3 7031.73 592.43
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Divided 6562.98 7242.37 1.10352
855 ero1-like. [refseq;acc:nm_014584]
secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] Subtracted 6439.3 7031.73 592.43
856 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 5734.15 6326.41 592.26
heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] Divided 5210.58 5749.33 1.1034
857 n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784]
phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674] Subtracted 6437.49 7029.22 591.73
858 dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] 6393.81 6984.94 591.13
n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] Divided 5210.58 5749.33 1.1034
859 heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [swissprot;acc:p52848]
nostrin. [refseq;acc:nm_052946] Subtracted 4682.87 4093.05 589.82
860 eap30 subunit of ell complex. [refseq;acc:nm_007241]
protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260] Divided 5210.58 5749.33 1.1034
861 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 5734.15 6326.41 1.10329
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Subtracted 4682.87 4093.05 589.82
862 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]
probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] Divided 4076.72 4497.74 1.10327
863 gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Subtracted 4682.87 4093.05 589.82
neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] Divided 5595.65 6173.23 1.10322
864 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Subtracted 4682.87 4093.05 589.82
ring finger protein 44. [refseq;acc:nm_014901] Divided 5595.65 6173.23 1.10322
865 15 kda selenoprotein precursor. [swissprot;acc:o60613] Subtracted 6344.41 6933.36 588.95

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/