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.


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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 [...,...].
Network Comparison Type Value Type Gene description Rank network_comparison Filtered Interaction Map red green
Results: HTML CSV LaTeX Showing element 2358 to 2407 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
description
Rank
network_comparison
red
green
reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] 1469 1.0195 207.013 211.05
retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329] 2224 1.00637 221.509 220.108
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 687 1.05602 132.413 125.389
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] 1012 1.03252 217.021 210.185
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] 1011 1.03253 217.026 210.189
retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] 1216 1.02513 218.269 212.918
retinoic acid receptor rxr-alpha. [swissprot;acc:p19793] 2759 1 0.00001 0.00001
retinoic acid receptor rxr-beta. [swissprot;acc:p28702] 3067
retinoic acid receptor rxr-gamma. [swissprot;acc:p48443] 2936
retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725] 1052 1.03097 211.449 217.998
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 187 1.14179 226.582 198.444
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 353 1.09694 231.73 211.252
rh type c glycoprotein. [refseq;acc:nm_016321] 1916 1.01016 196.88 198.88
rhesus blood group, b glycoprotein; rh type b glycoprotein. [refseq;acc:nm_020407] 1926 1.01008 196.925 198.91
rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [swissprot;acc:q02094] 1927 1.01006 196.932 198.914
rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] 786 1.04685 244.447 233.508
rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320] 1777 1.0121 216.878 214.286
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] 498 1.07172 220.161 235.95
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] 490 1.0719 220.183 236.015
rho interacting protein 3. [refseq;acc:nm_015134] 767 1.04874 213.803 224.224
rho-gtpase activating protein 10. [refseq;acc:nm_020824] 1386 1.02148 218.47 213.876
rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [swissprot;acc:q07960] 2480 1.00287 218.093 218.72
rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] 1266 1.02425 171.231 167.177
rho-gtpase-activating protein 8. [swissprot;acc:q9nsg0] 2479 1.00287 218.093 218.72
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 12 1.45259 337 232
ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477] 2093 1.00771 209.994 208.387
ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792] 1789 1.01205 210.997 213.539
ribonuclease iii (ec 3.1.26.3) (rnase iii) (p241). [swissprot;acc:q9nrr4] 3059 1 0.00001 0.00001
ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] 591 1.0633 216.72 230.439
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 590 1.06333 217.215 204.279
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 290 1.10428 231.969 210.064
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 313 1.10069 232.473 211.207
ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] 1836 1.01125 208.821 211.17
ribose-phosphate pyrophosphokinase i (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase i) (ppribp) (prs-i). [swissprot;acc:p09329] 2916 1 0.00001 0.00001
ribose-phosphate pyrophosphokinase ii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase ii) (ppribp) (prs-ii). [swissprot;acc:p11908] 3122
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] 2895
ribosomal protein l10-like protein. [refseq;acc:nm_080746] 358 1.09683 243.12 266.662
ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] 1998 1.00932 200.219 198.37
ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] 781 1.04798 245.84 257.636
ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] 1103 1.02846 229.441 235.972
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] 2165 1.00673 215.925 214.481
ribosomal protein s6 kinase alpha 2 (ec 2.7.1.37) (s6k-alpha 2) (90 kda ribosomal protein s6 kinase 2) (p90-rsk 2) (ribosomal s6 kinase 3) (rsk-3) (pp90rsk3). [swissprot;acc:q15349] 2171
ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [swissprot;acc:p51812] 2160
ribosomal protein s6 kinase alpha 6 (ec 2.7.1.37) (s6k-alpha 6) (90 kda ribosomal protein s6 kinase 6) (p90-rsk 6) (ribosomal s6 kinase 4) (rsk-4) (pp90rsk4). [swissprot;acc:q9uk32] 2170
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] 371 1.09447 186.52 170.42
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 372
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 2017 1.00907 127.397 128.553
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] 2262 1.00566 221.599 220.351
ring finger protein 20. [refseq;acc:nm_019592] 2388 1.0039 224.414 225.289
ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] 1588 1.01626 177.834 180.725

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/