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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1625 to 1674 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
407 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] Divided 1 239.75 260.544 1.08673
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Subtracted 0 10195.5 9856.7 338.8
neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] 1 237.109 254.667 17.558
udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537] Divided 0 9783.63 10111.2 1.03348
408 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Subtracted 10194.8 9856.12 338.68
ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Divided 1 255.112 234.804 1.08649
heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] Subtracted 237.109 254.667 17.558
udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855] Divided 0 9783.63 10111.2 1.03348
409 germ cell-less. [refseq;acc:nm_022471] Subtracted 10978.8 10644.4 334.4
rna polymerase i associated factor 53. [refseq;acc:nm_022490] Divided 1 241.045 261.874 1.08641
runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Subtracted 237.109 254.667 17.558
similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4] Divided 0 10598.5 10945.3 1.03272
410 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] Subtracted 10006.9 9676.53 330.37
e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] 1 237.109 254.667 17.558
histone h4. [swissprot;acc:p02304] Divided 0 9611.37 9308.99 1.03248
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] 1 233.376 253.539 1.0864
411 60s ribosomal protein l18. [swissprot;acc:q07020] Subtracted 237.109 254.667 17.558
60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] Divided 0 12115.7 12508.3 1.0324
tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] 1 233.376 253.539 1.0864
udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] Subtracted 0 9783.63 10111.2 327.57
412 5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] Divided 8546.06 8279.69 1.03217
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Subtracted 1 251.926 234.547 17.379
ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] Divided 240.788 261.416 1.08567
udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310] Subtracted 0 9783.63 10111.2 327.57
413 dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] Divided 1 240.913 261.45 1.08525
protein cgi-147. [swissprot;acc:q9y3e5] 0 5135.25 5298.12 1.03172
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Subtracted 1 223.202 205.9 17.302
udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133] 0 9783.63 10111.2 327.57
414 germ cell-less. [refseq;acc:nm_022471] Divided 10978.8 10644.4 1.03142
glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075] Subtracted 9783.63 10111.2 327.57
katanin p60 subunit a 1. [refseq;acc:nm_007044] Divided 1 232.431 252.238 1.08522
max protein. [swissprot;acc:p25912] Subtracted 227.828 210.561 17.267
415 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] Divided 232.382 252.166 1.08514
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] 0 13571.2 13166.3 1.03075
transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Subtracted 1 200.586 183.423 17.163
udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537] 0 9783.63 10111.2 327.57
416 dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] Divided 1 240.6 261.041 1.08496
tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Subtracted 200.791 183.66 17.131
transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] Divided 0 13607.6 13202 1.03072
udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855] Subtracted 9783.63 10111.2 327.57
417 huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 14570.4 14247.3 323.1
limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Divided 10854.8 10537.9 1.03007
set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] 1 233.539 253.197 1.08417
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Subtracted 235.94 218.837 17.103
418 alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 0 11186 10866.3 319.7
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Divided 16680.7 17180.3 1.02995
cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] 1 233.539 253.197 1.08417
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Subtracted 233.723 216.674 17.049
419 blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] Divided 0 16684 17183 1.02991
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Subtracted 14556.7 14237.8 318.9

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/