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 773 to 822 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
387 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] High confidence 242.238 264.11 1.09029
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Low confidence 200.057 192.938 1.0369
388 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 200.049 192.942 1.03683
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] High confidence 227.575 208.756 1.09015
389 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Low confidence 200.049 192.942 1.03683
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] High confidence 227.575 208.756 1.09015
390 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 241.828 263.62 1.09011
solute carrier family 35, member e2. [refseq;acc:nm_182838] Low confidence 203.647 211.144 1.03681
391 40s ribosomal protein s16. [swissprot;acc:p17008] High confidence 241.828 263.62 1.09011
serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Low confidence 200.046 192.943 1.03681
392 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] High confidence 241.83 263.615 1.09008
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Low confidence 200.894 193.766 1.03679
393 small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 201.334 194.242 1.03651
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] High confidence 225.719 207.072 1.09005
394 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Low confidence 204.815 197.606 1.03648
dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] High confidence 218.827 238.407 1.08948
395 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]
rna binding protein. [refseq;acc:nm_032509] Low confidence 206.88 199.607 1.03644
396 leptin receptor gene-related protein (ob-r gene related protein) (ob- rgrp). [swissprot;acc:o15243]
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] High confidence 240.801 262.34 1.08945
397 leptin receptor overlapping transcript-like 1 (my047 protein). [swissprot;acc:o95214] Low confidence 206.88 199.607 1.03644
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] High confidence 110.689 101.613 1.08932
398 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 218.818 238.358 1.0893
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Low confidence 205.997 213.496 1.0364
399 clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] High confidence 207.889 226.226 1.08821
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Low confidence 193.291 186.506 1.03638
400 phosducin-like protein (phlp). [swissprot;acc:q13371] High confidence 207.908 226.218 1.08807
solute carrier family 35, member e1. [refseq;acc:nm_024881] Low confidence 203.661 211.03 1.03618
401 replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] High confidence 207.908 226.218 1.08807
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Low confidence 205.017 197.863 1.03616
402 replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] High confidence 207.908 226.218 1.08807
x-linked protein sts1769. [swissprot;acc:q99871] Low confidence 211.253 203.883 1.03615
403 phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] High confidence 207.908 226.218 1.08807
three prime repair exonuclease 1 isoform c; deoxyribonuclease iii, dnaq/mutd (e. coli)-like; 3' repair exonuclease 1; atr interacting protein. [refseq;acc:nm_032166] Low confidence 211.253 203.883 1.03615
404 dna repair protein rad52 homolog. [swissprot;acc:p43351] High confidence 207.908 226.218 1.08807
metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Low confidence 203.081 196 1.03613
405 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] High confidence 207.931 226.209 1.0879
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Low confidence 203.081 196 1.03613
406 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 201.095 194.099 1.03604
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] High confidence 265.634 244.304 1.08731
407 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 239.75 260.544 1.08673
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Low confidence 201.123 194.127 1.03604
408 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] 207.558 200.363 1.03591
ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] High confidence 255.112 234.804 1.08649
409 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Low confidence 149.423 144.256 1.03582
rna polymerase i associated factor 53. [refseq;acc:nm_022490] High confidence 241.045 261.874 1.08641
410 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] 233.376 253.539 1.0864
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Low confidence 202.074 195.097 1.03576
411 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] 214.628 222.301 1.03575
tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] High confidence 233.376 253.539 1.0864

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/