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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description Rank Gene Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 801 to 850 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
description
Rank
red
green
network_comparison
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 1881 210.592 208.355 1.01074
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] 1329 218.509 213.648 1.02275
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] 1326
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 339 243.583 267.527 1.0983
dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] 1029 222.364 215.535 1.03168
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] 906 230.764 239.62 1.03838
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] 905 230.768 239.632 1.03841
dna excision repair protein ercc-1. [swissprot;acc:p07992] 3216 0.00001 0.00001 1
dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] 2515 215.835 216.341 1.00234
dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273] 2517
dna ligase i (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p18858] 3103 0.00001 0.00001 1
dna ligase iv (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p49917] 2808
dna methyltransferase 1-associated protein 1 (dnmt1-associated protein 1) (dnmap1). [swissprot;acc:q9npf5] 2796
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 1878 212.186 214.467 1.01075
dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] 1749 206.058 203.485 1.01264
dna mismatch repair protein msh2. [swissprot;acc:p43246] 3151 0.00001 0.00001 1
dna mismatch repair protein msh6 (muts-alpha 160 kda subunit) (g/t mismatch binding protein) (gtbp) (gtmbp) (p160). [swissprot;acc:p52701] 3045
dna polymerase delta p38 subunit. [refseq;acc:nm_015584] 1872 222.819 225.228 1.01081
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 176 275.754 235.908 1.1689
dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] 1447 250.854 255.842 1.01988
dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] 1615 246.38 242.596 1.0156
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] 694 241.907 229.35 1.05475
dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] 2074 216.324 214.599 1.00804
dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609] 2345 219.878 218.893 1.0045
dna repair protein rad52 homolog. [swissprot;acc:p43351] 404 207.908 226.218 1.08807
dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] 1891 233.828 231.395 1.01051
dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [swissprot;acc:p33992] 1673 228.496 231.729 1.01415
dna replication licensing factor mcm8 (minichromosome maintenance 8). [swissprot;acc:q9uja3] 3011 0.00001 0.00001 1
dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135] 1681 216.899 213.889 1.01407
dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] 1790 203.759 201.349 1.01197
dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] 1796 201.357 1.01193
dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] 2015 217.941 215.979 1.00908
dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] 1840 211.882 209.544 1.01116
dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989] 2684 208.438 208.635 1.00095
dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] 817 212.386 221.785 1.04425
dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] 416 240.6 261.041 1.08496
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 1071 231.277 238.356 1.03061
dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 413 240.913 261.45 1.08525
dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] 377 242.691 265.481 1.09391
dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] 896 230.811 239.785 1.03888
dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] 780 232.762 243.933 1.04799
dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] 819 228.563 238.668 1.04421
dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] 364 243.208 266.617 1.09625
dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] 688 237.554 250.823 1.05586
dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] 676 232.469 245.613 1.05654
dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] 427 239.977 259.525 1.08146
dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] 424 240.287 260.193 1.08284
dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] 538 237.627 253.604 1.06724
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] 327 243.817 267.962 1.09903
dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] 375 242.686 265.516 1.09407

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/