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 12864 to 12913 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1106 vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] Ranked Subtracted 218.484 212.675 5.809
1107 calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [swissprot;acc:q13555] Squared 28606.2 31850.3 3244.1
cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] Rooted Divided 61.5152 64.5623 1.04953
dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] Subtracted 67.2521 70.3462 3.0941
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] Squared Divided 24175.6 27657.3 1.14402
phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] Measured 5489.99 5986.63 1.09046
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] Ranked 204.603 210.324 1.02796
transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594] Measured Subtracted 7433.73 7950.61 516.88
vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] Ranked 218.483 212.676 5.807
1108 calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [swissprot;acc:q13557] Squared 28606.2 31850.3 3244.1
flotillin-1. [swissprot;acc:o75955] Rooted Divided 61.5152 64.5623 1.04953
interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] Ranked 218.006 212.119 1.02775
nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [swissprot;acc:q14494] Measured Subtracted 7433.73 7950.61 516.88
protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260] Squared Divided 24175.6 27657.3 1.14402
rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] Measured 4846.16 5283.08 1.09016
transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] Rooted Subtracted 58.8683 61.9622 3.0939
vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864] Ranked 218.481 212.675 5.806
1109 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Rooted 67.2519 70.3434 3.0915
epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204] Ranked 221.939 216.143 5.796
mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [swissprot;acc:o95382] Squared 28606.2 31850.3 3244.1
myb-related protein b (b-myb). [swissprot;acc:p10244] Divided 22817.9 26093.4 1.14355
nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289] Measured Subtracted 7433.73 7950.61 516.88
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] Divided 6545.19 7132.89 1.08979
sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] Rooted 61.5152 64.5622 1.04953
translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] Ranked 218.098 212.209 1.02775
1110 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] 216.78 222.782 1.02769
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Subtracted 159.13 164.917 5.787
mstp028 protein. [refseq;acc:nm_031954] Measured 5838.87 6355.06 516.19
nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] Divided 5947.53 6481.56 1.08979
serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269] Squared 25660.4 29342.7 1.1435
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Rooted 68.6067 72.0041 1.04952
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] Squared Subtracted 28606.2 31850.3 3244.1
sqv-7-like protein (fragment). [sptrembl;acc:o95454] Rooted 60.9994 57.9085 3.0909
1111 60s ribosomal protein l21. [swissprot;acc:p46778] 60.1366 63.2237 3.0871
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Ranked Divided 217.99 212.123 1.02766
armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] Rooted 68.4309 71.8158 1.04946
basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Ranked Subtracted 159.165 164.951 5.786
putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Measured 5393.37 5909.47 516.1
rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] Divided 6540.61 7127.41 1.08972
ribosomal protein s6 kinase alpha 1 (ec 2.7.1.37) (s6k-alpha 1) (90 kda ribosomal protein s6 kinase 1) (p90-rsk 1) (ribosomal s6 kinase 1) (rsk-1) (pp90rsk1). [swissprot;acc:q15418] Squared Subtracted 28606.2 31850.3 3244.1
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] Divided 59331.2 67833.7 1.14331
1112 atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288] Subtracted 28606.2 31850.3 3244.1
epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] Ranked 221.93 216.146 5.784
hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] Divided 251.863 258.829 1.02766
histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Rooted 68.4309 71.8157 1.04946
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Measured 5910.54 6440.58 1.08968
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Rooted Subtracted 59.0741 62.1501 3.076
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] Measured 5840.01 6355.56 515.55
syntaxin 6. [swissprot;acc:o43752] Squared Divided 26720.4 30548.3 1.14326
1113 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] Rooted Subtracted 61.6272 64.6988 3.0716

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/