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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Rank Gene Interaction Map Value Type description Filtered red Network Comparison Type green network_comparison
Results: HTML CSV LaTeX Showing element 12864 to 12913 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
Network Comparison Type
green
network_comparison
1106 Rooted highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] 55.2209 Subtracted 52.1262 3.0947
1107 Measured phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] 5489.99 Divided 5986.63 1.09046
transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594] 7433.73 Subtracted 7950.61 516.88
Ranked 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] 204.603 Divided 210.324 1.02796
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] 218.483 Subtracted 212.676 5.807
Squared 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] 28606.2 31850.3 3244.1
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] 24175.6 Divided 27657.3 1.14402
Rooted cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] 61.5152 64.5623 1.04953
dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] 67.2521 Subtracted 70.3462 3.0941
1108 Measured 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] 7433.73 7950.61 516.88
rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] 4846.16 Divided 5283.08 1.09016
Ranked interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] 218.006 212.119 1.02775
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] 218.481 Subtracted 212.675 5.806
Squared 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] 28606.2 31850.3 3244.1
protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260] 24175.6 Divided 27657.3 1.14402
Rooted flotillin-1. [swissprot;acc:o75955] 61.5152 64.5623 1.04953
transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] 58.8683 Subtracted 61.9622 3.0939
1109 Measured nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289] 7433.73 7950.61 516.88
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] 6545.19 Divided 7132.89 1.08979
Ranked 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] 221.939 Subtracted 216.143 5.796
translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] 218.098 Divided 212.209 1.02775
Squared mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [swissprot;acc:o95382] 28606.2 Subtracted 31850.3 3244.1
myb-related protein b (b-myb). [swissprot;acc:p10244] 22817.9 Divided 26093.4 1.14355
Rooted dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] 67.2519 Subtracted 70.3434 3.0915
sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] 61.5152 Divided 64.5622 1.04953
1110 Measured mstp028 protein. [refseq;acc:nm_031954] 5838.87 Subtracted 6355.06 516.19
nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] 5947.53 Divided 6481.56 1.08979
Ranked 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] 159.13 Subtracted 164.917 5.787
Squared 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] 25660.4 Divided 29342.7 1.1435
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] 28606.2 Subtracted 31850.3 3244.1
Rooted 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] 68.6067 Divided 72.0041 1.04952
sqv-7-like protein (fragment). [sptrembl;acc:o95454] 60.9994 Subtracted 57.9085 3.0909
1111 Measured putative sialoglycoprotease type 2. [refseq;acc:nm_022353] 5393.37 5909.47 516.1
rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] 6540.61 Divided 7127.41 1.08972
Ranked apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 217.99 212.123 1.02766
basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] 159.165 Subtracted 164.951 5.786
Squared 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] 28606.2 31850.3 3244.1
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] 59331.2 Divided 67833.7 1.14331
Rooted 60s ribosomal protein l21. [swissprot;acc:p46778] 60.1366 Subtracted 63.2237 3.0871
armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] 68.4309 Divided 71.8158 1.04946
1112 Measured putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] 5910.54 6440.58 1.08968
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] 5840.01 Subtracted 6355.56 515.55
Ranked epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] 221.93 216.146 5.784
hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] 251.863 Divided 258.829 1.02766
Squared atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288] 28606.2 Subtracted 31850.3 3244.1
syntaxin 6. [swissprot;acc:o43752] 26720.4 Divided 30548.3 1.14326
Rooted histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] 68.4309 71.8157 1.04946
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] 59.0741 Subtracted 62.1501 3.076
1113 Measured phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] 5910.54 Divided 6440.58 1.08968

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/