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 4477 to 4526 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2239 2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953] Subtracted 5783.76 6048.94 265.18
sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637] Divided 5902.27 6181.21 1.04726
2240 ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316] Subtracted 5783.76 6048.94 265.18
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Divided 5902.27 6181.21 1.04726
2241 phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] Subtracted 5783.75 6048.93 265.18
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Divided 3670.45 3504.91 1.04723
2242 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] Subtracted 5783.71 6048.89 265.18
2243 inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Divided 5776.96 6049.61 1.0472
membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] Subtracted 5783.76 6048.94 265.18
2244 gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915] Divided 5776.96 6049.61 1.0472
polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599] Subtracted 5783.76 6048.94 265.18
2245 growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861] 5783.73 6048.91
inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] Divided 5776.96 6049.61 1.0472
2246 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 6209.77 6501.99 1.04706
eyes absent homolog 3. [swissprot;acc:q99504] Subtracted 5779.66 6044.78 265.12
2247 eyes absent homolog 4. [swissprot;acc:o95677] 5784.9 6049.99 265.09
rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062] Divided 5819.36 6092.93 1.04701
2248 eyes absent homolog 2. [swissprot;acc:o00167] Subtracted 5786.15 6050.71 264.56
signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624] Divided 5833.01 6106.48 1.04688
2249 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 6834.03 7153.66 1.04677
myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572] Subtracted 6711.27 6974.49 263.22
2250 esterase d (ec 3.1.1.1). [swissprot;acc:p10768] Divided 6834.03 7153.66 1.04677
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] Subtracted 6707.29 6970.07 262.78
2251 hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775]
serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270] Divided 6196.65 6486.12 1.04671
2252 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] 5840.54 6113.01 1.04665
ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] Subtracted 4806.38 5067 260.62
2253 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 4806.33 5066.92 260.59
mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Divided 3629.21 3467.48 1.04664
2254 alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 7383.13 7727.39 1.04663
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Subtracted 4632.65 4892.66 260.01
2255 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] Divided 3624.59 3463.37 1.04655
m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305] Subtracted 4383.34 4642.93 259.59
2256 early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566] 4871.11 5129.63 258.52
ubiquitin. [swissprot;acc:p02248] Divided 7390.36 7733.85 1.04648
2257 sr rich protein. [refseq;acc:nm_032870] 6245.32 6534.23 1.04626
visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235] Subtracted 5259.97 5518.26 258.29
2258 60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] Divided 5150.31 5388.05 1.04616
neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076] Subtracted 5259.1 5517.22 258.12
2259 neurocalcin delta. [swissprot;acc:p29554] 5258.96 5517.06 258.1
ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554] Divided 6486.84 6786.23 1.04615
2260 block 23. [sptrembl;acc:q8nhw5] 5150.14 5387.84
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Subtracted 3687.37 3429.37 258
2261 38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318] Divided 6486.84 6786.23 1.04615
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Subtracted 3688.8 3431.33 257.47
2262 fas apoptotic inhibitory molecule. [refseq;acc:nm_018147] 5666.91 5923.48 256.57
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] Divided 5148.88 5386.34 1.04612
2263 40s ribosomal protein s3a. [swissprot;acc:p49241] 4918.64 5145.39 1.0461
lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234] Subtracted 6327.14 6579.38 252.24

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/