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.


Navigation/Query Panel:
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 [...,...].
Gene Rank Value Type description Interaction Map Network Comparison Type green Filtered network_comparison red
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 19268 in total
Value Type  : Ranked
Rank
description
Interaction Map
Network Comparison Type
green
Filtered
network_comparison
red
398 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] High confidence Divided 238.358 1 1.0893 218.818
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Subtracted 10320.9 0 367.51 9953.39
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] 226.218 1 18.31 207.908
pr-domain zinc finger protein 16 (transcription factor mel1). [swissprot;acc:q9haz2] Low confidence Divided 13468.5 0 1.08217 12445.8
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] 213.496 1 1.0364 205.997
399 carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] High confidence Subtracted 7311 0 359 7670
clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Divided 226.226 1 1.08821 207.889
dna repair protein rad52 homolog. [swissprot;acc:p43351] Subtracted 226.218 18.31 207.908
glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Divided 17271.4 0 1.03402 16703.1
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Low confidence Subtracted 10629.5 626.9 10002.6
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Divided 13511.7 1.08207 12486.9
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] Subtracted 197.863 1 7.154 205.017
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Divided 186.506 1.03638 193.291
400 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] High confidence Subtracted 226.209 18.278 207.931
dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] Low confidence 11010.5 0 625.9 10384.6
glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] High confidence 12224.2 357.5 12581.7
glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Divided 17278.4 1.03395 16711
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Low confidence Subtracted 193.766 1 7.128 200.894
phosducin-like protein (phlp). [swissprot;acc:q13371] High confidence Divided 226.218 1.08807 207.908
solute carrier family 35, member e1. [refseq;acc:nm_024881] Low confidence 211.03 1.03618 203.661
syntaxin 10 (syn10). [swissprot;acc:o60499] 12247.2 0 1.08203 11318.7
401 mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932] High confidence Subtracted 20558 356 20914
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] 236.224 1 18.21 254.434
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] Divided 226.218 1.08807 207.908
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Low confidence 10971.5 0 1.08151 11865.8
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Subtracted 192.938 1 7.119 200.057
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] Divided 197.863 1.03616 205.017
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] High confidence 11904.9 0 1.03368 12305.9
ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] Low confidence Subtracted 11832.5 620.1 11212.4
402 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Divided 10979.9 1.08108 11870.1
adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] High confidence 10918 1.03367 10562.4
Subtracted 355.6
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] 249.983 1 18.181 231.802
microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650] Low confidence 8815 0 616 9431
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] High confidence Divided 226.218 1 1.08807 207.908
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Low confidence Subtracted 203.181 7.111 210.292
x-linked protein sts1769. [swissprot;acc:q99871] Divided 203.883 1.03615 211.253
403 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 11825.8 0 1.08063 12779.3
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Subtracted 11580 613.5 10966.5
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] High confidence 246.338 1 17.87 228.468
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Divided 226.218 1.08807 207.908
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Low confidence Subtracted 192.942 7.107 200.049
scribble. [refseq;acc:nm_015356] High confidence 12719 0 348.5 12370.5
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 Divided 203.883 1 1.03615 211.253
udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] High confidence 10111.2 0 1.03348 9783.63
404 ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560] Low confidence 12572.4 1.07839 11658.5
bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] High confidence Subtracted 246.33 1 17.867 228.463
dna repair protein rad52 homolog. [swissprot;acc:p43351] Divided 226.218 1.08807 207.908
enigma protein; lim domain protein. [refseq;acc:nm_005451] Low confidence Subtracted 12940.6 0 611.6 13552.2
metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Divided 196 1 1.03613 203.081

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/