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 description Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 630 to 679 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
Interaction Map
red
green
network_comparison
158 dnaj homolog subfamily c member 8 (splicing protein spf31) (hspc315). [swissprot;acc:o75937] DNAJC8 Divided Low confidence 219.838 207.417 1.05988
mosaic protein lgn. [swissprot;acc:p81274] GPSM2 High confidence 249.663 298.263 1.19466
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] FER Subtracted Low confidence 216.796 205.073 11.723
159 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] RPL29 216.79 205.07 11.72
c3hc4-type zinc finger protein; likely ortholog of mouse dioxin inducible factor 3. [refseq;acc:nm_024835] GGNBP2 Divided 219.838 207.417 1.05988
doc-1 related protein (doc-1r). [swissprot;acc:o75956] CDK2AP2 Subtracted High confidence 312 284 28
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] RGS17 Divided 249.663 298.263 1.19466
160 adenomatous polyposis coli protein (apc protein). [swissprot;acc:p25054] APC Low confidence 222.31 235.538 1.0595
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] GNAO1 High confidence 249.663 298.263 1.19466
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] NEUROD6 Subtracted 312 284 28
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] FES Low confidence 216.783 205.066 11.717
161 adenomatous polyposis coli like. [refseq;acc:nm_005883] APC2 Divided 222.34 235.547 1.0594
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] FOXP1 Subtracted 219.6 207.907 11.693
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] NEUROD1 High confidence 312 284 28
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] RAP1GAP Divided 249.663 298.263 1.19466
162 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] no value Subtracted 142 170 28
defender against cell death 1 (dad-1). [swissprot;acc:p46966] DAD1 Divided Low confidence 197.99 186.913 1.05926
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] FOXP4 Subtracted 219.593 207.903 11.69
nostrin. [refseq;acc:nm_052946] NOSTRIN Divided High confidence 209.299 249.187 1.19058
163 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] ARRB2 Subtracted 133 105 28
eap30 subunit of ell complex. [refseq;acc:nm_007241] SNF8 Divided 209.299 249.187 1.19058
ribonuclease p protein subunit p20 (ec 3.1.26.5) (rnasep protein p20) (hpop7). [swissprot;acc:o75817] POP7 Subtracted Low confidence 209.954 221.607 11.653
vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] VPS41 Divided 202.698 191.393 1.05907
164 3'(2'), 5'-bisphosphate nucleotidase 1; bisphosphate 3'-nucleotidase; bpntase; pap-inositol-1,4-phosphatase. [refseq;acc:nm_006085] BPNT1 Subtracted 209.954 221.607 11.653
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] ARRB1 High confidence 133 105 28
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] SLC39A6 Divided 209.299 249.187 1.19058
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] PPM1B Low confidence 196.714 185.758 1.05898
165 60s ribosomal protein l6 (tax-responsive enhancer element binding protein 107) (taxreb107) (neoplasm-related protein c140). [swissprot;acc:q02878] RPL6 Subtracted 209.954 221.607 11.653
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] CAPN1 Divided 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] GAD2 High confidence 209.299 249.187 1.19058
spermatogenesis associated 6. [refseq;acc:nm_019073] SPATA6 Subtracted 133 105 28
166 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] CAPN2 Divided Low confidence 222.502 210.342 1.05781
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] NAPG High confidence 209.299 249.187 1.19058
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] NEUROD4 Subtracted 312 284 28
tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] TNS3 Low confidence 219.336 207.703 11.633
167 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] AMPD2 High confidence 133 105 28
glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] GAD1 Divided 209.299 249.187 1.19058
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] RHOBTB2 Low confidence 212.695 201.131 1.05749
Subtracted 11.564
168 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] CHD5 High confidence 312 284 28
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] no value Divided 82.5916 98.0548 1.18722
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] FER Low confidence 216.796 205.073 1.05717
protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] DCHS1 Subtracted 218.925 207.441 11.484
169 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] RPL29 Divided 216.79 205.07 1.05715
apg3p; pc3-96 protein. [refseq;acc:nm_022488] ATG3 High confidence 82.5916 98.0548 1.18722
cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] CDK2AP1 Subtracted 312 284 28
f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] CAPZA1 Low confidence 213.671 202.205 11.466
170 huntingtin interacting protein c. [refseq;acc:nm_012272] PRPF40B High confidence 227.971 200.417 27.554
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] TIA1 Divided 227.199 192.715 1.17894
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] FES Low confidence 216.783 205.066 1.05714

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
- Hugo is the HGNC identifier if it exists
- 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/