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 Network Comparison Type Value Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 501 to 550 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
network_comparison
green
126 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Divided High confidence 94 1.21277 114
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Subtracted 285.684 33.45 252.234
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Divided Low confidence 191.688 1.06707 179.639
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Subtracted 226.892 13.231 213.661
127 adenomatous polyposis coli protein (apc protein). [swissprot;acc:p25054] 222.31 13.228 235.538
cullin homolog 2 (cul-2). [swissprot;acc:q13617] High confidence 285.684 33.45 252.234
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Divided 94 1.21277 114
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Low confidence 203.678 1.06705 190.88
128 adenomatous polyposis coli like. [refseq;acc:nm_005883] Subtracted 222.34 13.207 235.547
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Divided High confidence 94 1.21277 114
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Subtracted 285.684 33.45 252.234
striatin. [swissprot;acc:o43815] Divided Low confidence 214.085 1.06618 200.796
129 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Subtracted High confidence 285.684 33.45 252.234
goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Divided Low confidence 220.969 1.06609 235.572
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] High confidence 94 1.21277 114
transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] Subtracted Low confidence 218.561 13.13 205.431
130 neuronal protein np25. [swissprot;acc:q9ui15] 218.66 13.09 205.57
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] High confidence 242.735 33.324 276.059
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Divided 94 1.21277 114
striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] Low confidence 225.495 1.06602 211.529
131 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Subtracted High confidence 242.718 33.3 276.018
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Divided 294.053 1.21228 242.562
striatin 4 (zinedin). [swissprot;acc:q9nrl3] Low confidence 213.878 1.065 200.825
Subtracted 13.053
132 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Divided 220.268 1.06411 206.997
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Subtracted High confidence 229.406 32.711 196.695
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Low confidence 203.016 13.051 189.965
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Divided High confidence 350 1.2069 290
133 formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Subtracted 226.887 32.167 194.72
prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Divided Low confidence 220.268 1.06411 206.997
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Subtracted 203.007 13.022 189.985
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Divided High confidence 350 1.2069 290
134 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Subtracted 226.884 32.094 194.79
transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] Divided Low confidence 218.561 1.06391 205.431
transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] Subtracted 218.36 12.96 205.4
135 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Divided High confidence 350 1.2069 290
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Subtracted 263.215 31.808 231.407
neuronal protein np25. [swissprot;acc:q9ui15] Divided Low confidence 218.66 1.06368 205.57
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Subtracted 202.96 12.866 190.094
136 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Divided High confidence 350 1.2069 290
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Subtracted 263.215 31.808 231.407
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Divided Low confidence 202.996 1.06362 190.854
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Subtracted 219.344 12.824 206.52
137 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] High confidence 263.191 31.797 231.394
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Divided 350 1.2069 290
testican-3 precursor. [swissprot;acc:q9bq16] Low confidence 220.395 1.0635 234.389
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Subtracted 203.678 12.798 190.88
138 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] High confidence 174.667 30.889 205.556
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Low confidence 219.273 12.766 206.507

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/