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 Filtered description Value Type Interaction Map Gene Network Comparison Type red green network_comparison
Results: HTML CSV LaTeX Showing element 651 to 700 of 9634 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Rank
Filtered
description
Interaction Map
red
green
network_comparison
163 1 eap30 subunit of ell complex. [refseq;acc:nm_007241] High confidence 209.299 249.187 1.19058
vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] Low confidence 202.698 191.393 1.05907
164 0 dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] High confidence 11971.7 10412.4 1.14975
zinc finger protein 95 homolog (zfp-95). [swissprot;acc:q9y2l8] Low confidence 4238.74 4834.52 1.14056
1 liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] High confidence 209.299 249.187 1.19058
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Low confidence 196.714 185.758 1.05898
165 0 ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] High confidence 13255.4 15183.2 1.14544
zinc finger protein 80 (znfpt17). [swissprot;acc:p51504] Low confidence 4239.56 4835.4 1.14054
1 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 222.508 210.345 1.05782
glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] High confidence 209.299 249.187 1.19058
166 0 my016 protein. [sptrembl;acc:q9h3k6] 5561.19 6366.91 1.14488
zinc finger protein 187. [refseq;acc:nm_152736] Low confidence 4240.02 4835.88 1.14053
1 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] 222.502 210.342 1.05781
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] High confidence 209.299 249.187 1.19058
167 0 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 12157.6 13890.3 1.14252
zinc finger protein 302 (znf135-like) (znf140-like). [swissprot;acc:q9nr11] Low confidence 4240.02 4835.88 1.14053
1 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] High confidence 209.299 249.187 1.19058
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Low confidence 212.695 201.131 1.05749
168 0 fos-related antigen 2. [swissprot;acc:p15408] High confidence 7091.75 6217.28 1.14065
zinc finger protein zfp6 (fragment). [sptrembl;acc:q92967] Low confidence 4240.65 4836.56 1.14052
1 gaba-a receptor-associated protein. [sptrembl;acc:q9by60] High confidence 82.5916 98.0548 1.18722
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Low confidence 216.796 205.073 1.05717
169 0 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] High confidence 9875.43 11256.8 1.13988
zinc finger protein 8 (zinc finger protein hf.18) (fragment). [swissprot;acc:p17098] Low confidence 4241.01 4836.94 1.14052
1 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] 216.79 205.07 1.05715
apg3p; pc3-96 protein. [refseq;acc:nm_022488] High confidence 82.5916 98.0548 1.18722
170 0 b-lymphocyte activation-related protein. [sptrembl;acc:q96pn3] Low confidence 4241.64 4837.61 1.1405
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] High confidence 11364 12941 1.13877
1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 227.199 192.715 1.17894
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Low confidence 216.783 205.066 1.05714
171 0 lamin b2. [swissprot;acc:q03252] High confidence 12135.4 13802 1.13733
zinc finger protein 169 (fragment). [swissprot;acc:q14929] Low confidence 4242.53 4838.56 1.14049
1 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 219.889 208.064 1.05683
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] High confidence 227.202 192.823 1.17829
172 0 zinc finger protein 350; zinc-finger protein zbrk1. [refseq;acc:nm_021632] Low confidence 4244.56 4840.72 1.14045
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] High confidence 12225.7 13893.1 1.13638
1 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 174.667 205.556 1.17685
f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Low confidence 213.671 202.205 1.0567
173 0 suppressor of actin 1. [refseq;acc:nm_014016] High confidence 19088.1 16804.6 1.13589
zinc finger protein 223. [swissprot;acc:q9uk11] Low confidence 4245 4841.18 1.14044
1 sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 221.678 209.795 1.05664
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] High confidence 227.032 193.056 1.17599
174 0 ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] 13248.5 11666.4 1.13561
similar to zinc finger protein 20 (zinc finger protein kox13) (dkfzp572p0920). [refseq;acc:nm_145233] Low confidence 4244.83 4840.99 1.14044
1 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] High confidence 335 286 1.17133
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Low confidence 219.6 207.907 1.05624
175 0 thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] High confidence 13248.5 11666.4 1.13561
zinc finger protein 222. [swissprot;acc:q9uk12] Low confidence 4244.83 4840.99 1.14044
1 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] High confidence 199.949 234.187 1.17123
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Low confidence 219.593 207.903 1.05623

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/