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 Filtered Rank Value Type description Network Comparison Type Interaction Map green red network_comparison
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 19268 in total
Filtered  : 1
Value Type  : Ranked
Rank
description
Network Comparison Type
Interaction Map
green
red
network_comparison
123 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Divided Low confidence 190.094 202.96 1.06768
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted High confidence 193.056 227.032 33.976
striatin. [swissprot;acc:o43815] Low confidence 200.796 214.085 13.289
124 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 206.997 220.268 13.271
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 High confidence 171.595 208.52 1.21519
natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Low confidence 210.566 224.763 1.06742
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted High confidence 252.234 285.684 33.45
125 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Divided Low confidence 227.616 213.243 1.0674
high-mobility group 20a. [refseq;acc:nm_018200] High confidence 171.778 208.588 1.21429
prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Subtracted Low confidence 206.997 220.268 13.271
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] High confidence 252.234 285.684 33.45
126 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Divided 114 94 1.21277
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 252.234 285.684 33.45
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Divided Low confidence 179.639 191.688 1.06707
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 213.661 226.892 13.231
127 adenomatous polyposis coli protein (apc protein). [swissprot;acc:p25054] 235.538 222.31 13.228
cullin homolog 2 (cul-2). [swissprot;acc:q13617] High confidence 252.234 285.684 33.45
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Divided 114 94 1.21277
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Low confidence 190.88 203.678 1.06705
128 adenomatous polyposis coli like. [refseq;acc:nm_005883] Subtracted 235.547 222.34 13.207
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Divided High confidence 114 94 1.21277
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Subtracted 252.234 285.684 33.45
striatin. [swissprot;acc:o43815] Divided Low confidence 200.796 214.085 1.06618
129 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Subtracted High confidence 252.234 285.684 33.45
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 235.572 220.969 1.06609
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] High confidence 114 94 1.21277
transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] Subtracted Low confidence 205.431 218.561 13.13
130 neuronal protein np25. [swissprot;acc:q9ui15] 205.57 218.66 13.09
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] High confidence 276.059 242.735 33.324
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Divided 114 94 1.21277
striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] Low confidence 211.529 225.495 1.06602
131 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Subtracted High confidence 276.018 242.718 33.3
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 242.562 294.053 1.21228
striatin 4 (zinedin). [swissprot;acc:q9nrl3] Low confidence 200.825 213.878 1.065
Subtracted 13.053
132 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Divided 206.997 220.268 1.06411
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Subtracted High confidence 196.695 229.406 32.711
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Low confidence 189.965 203.016 13.051
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Divided High confidence 290 350 1.2069
133 formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Subtracted 194.72 226.887 32.167
prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Divided Low confidence 206.997 220.268 1.06411
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Subtracted 189.985 203.007 13.022
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Divided High confidence 290 350 1.2069
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 194.79 226.884 32.094
transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] Divided Low confidence 205.431 218.561 1.06391
transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] Subtracted 205.4 218.36 12.96
135 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Divided High confidence 290 350 1.2069
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Subtracted 231.407 263.215 31.808
neuronal protein np25. [swissprot;acc:q9ui15] Divided Low confidence 205.57 218.66 1.06368

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/