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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Gene Rank Value Type Network Comparison Type green network_comparison description Interaction Map red Filtered
Results: HTML CSV LaTeX Showing element 12864 to 12913 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
Network Comparison Type
green
network_comparison
description
red
1106 Rooted Subtracted 52.1262 3.0947 highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] 55.2209
1107 Measured Divided 5986.63 1.09046 phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] 5489.99
Subtracted 7950.61 516.88 transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594] 7433.73
Ranked Divided 210.324 1.02796 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
Subtracted 212.676 5.807 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
Squared Divided 27657.3 1.14402 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
Subtracted 31850.3 3244.1 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
Rooted Divided 64.5623 1.04953 cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] 61.5152
Subtracted 70.3462 3.0941 dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] 67.2521
1108 Measured Divided 5283.08 1.09016 rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] 4846.16
Subtracted 7950.61 516.88 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
Ranked Divided 212.119 1.02775 interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] 218.006
Subtracted 212.675 5.806 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
Squared Divided 27657.3 1.14402 protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260] 24175.6
Subtracted 31850.3 3244.1 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
Rooted Divided 64.5623 1.04953 flotillin-1. [swissprot;acc:o75955] 61.5152
Subtracted 61.9622 3.0939 transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] 58.8683
1109 Measured Divided 7132.89 1.08979 rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] 6545.19
Subtracted 7950.61 516.88 nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289] 7433.73
Ranked Divided 212.209 1.02775 translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] 218.098
Subtracted 216.143 5.796 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
Squared Divided 26093.4 1.14355 myb-related protein b (b-myb). [swissprot;acc:p10244] 22817.9
Subtracted 31850.3 3244.1 mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [swissprot;acc:o95382] 28606.2
Rooted Divided 64.5622 1.04953 sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] 61.5152
Subtracted 70.3434 3.0915 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] 67.2519
1110 Measured Divided 6481.56 1.08979 nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] 5947.53
Subtracted 6355.06 516.19 mstp028 protein. [refseq;acc:nm_031954] 5838.87
Ranked Divided 222.782 1.02769 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] 216.78
Subtracted 164.917 5.787 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 159.13
Squared Divided 29342.7 1.1435 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
Subtracted 31850.3 3244.1 signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] 28606.2
Rooted Divided 72.0041 1.04952 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
Subtracted 57.9085 3.0909 sqv-7-like protein (fragment). [sptrembl;acc:o95454] 60.9994
1111 Measured Divided 7127.41 1.08972 rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] 6540.61
Subtracted 5909.47 516.1 putative sialoglycoprotease type 2. [refseq;acc:nm_022353] 5393.37
Ranked Divided 212.123 1.02766 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 217.99
Subtracted 164.951 5.786 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] 159.165
Squared Divided 67833.7 1.14331 steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] 59331.2
Subtracted 31850.3 3244.1 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
Rooted Divided 71.8158 1.04946 armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] 68.4309
Subtracted 63.2237 3.0871 60s ribosomal protein l21. [swissprot;acc:p46778] 60.1366
1112 Measured Divided 6440.58 1.08968 putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] 5910.54
Subtracted 6355.56 515.55 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
Ranked Divided 258.829 1.02766 hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] 251.863
Subtracted 216.146 5.784 epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] 221.93
Squared Divided 30548.3 1.14326 syntaxin 6. [swissprot;acc:o43752] 26720.4
Subtracted 31850.3 3244.1 atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288] 28606.2
Rooted Divided 71.8157 1.04946 histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] 68.4309
Subtracted 62.1501 3.076 signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] 59.0741
1113 Measured Divided 6440.58 1.08968 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

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/