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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 625 to 674 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
157 brain protein 44. [swissprot;acc:o95563] Squared 89182.8 125229 1.40418
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Rooted 52.7582 61.9123 1.17351
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Measured 23693.7 18263 1.29736
transcription factor lbx1. [swissprot;acc:p52954] Ranked 249.663 298.263 1.19466
158 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Rooted 56.3507 66.1252 1.17346
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Measured 23693.7 18263 1.29736
mosaic protein lgn. [swissprot;acc:p81274] Ranked 249.663 298.263 1.19466
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Squared 89182.8 125229 1.40418
159 necdin. [swissprot;acc:q99608] Measured 23693.7 18263 1.29736
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Ranked 249.663 298.263 1.19466
rna-binding protein. [refseq;acc:nm_019027] Rooted 52.7642 61.9019 1.17318
septin 6. [swissprot;acc:q14141] Squared 88953.6 124854 1.40359
160 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Rooted 52.7642 61.9019 1.17318
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Ranked 249.663 298.263 1.19466
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Squared 173408 242989 1.40126
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Measured 23693.7 18263 1.29736
161 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Squared 173408 242989 1.40126
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Measured 23693.7 18263 1.29736
ns1-associated protein 1. [refseq;acc:nm_006372] Rooted 52.7642 61.9019 1.17318
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Ranked 249.663 298.263 1.19466
162 heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Rooted 52.7642 61.9019 1.17318
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Squared 173408 242989 1.40126
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Measured 23693.7 18263 1.29736
nostrin. [refseq;acc:nm_052946] Ranked 209.299 249.187 1.19058
163 eap30 subunit of ell complex. [refseq;acc:nm_007241]
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Rooted 52.7702 61.8915 1.17285
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Squared 173408 242989 1.40126
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Measured 23693.7 18263 1.29736
164 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Squared 173408 242989 1.40126
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Ranked 209.299 249.187 1.19058
mad protein (max dimerizer). [swissprot;acc:q05195] Rooted 55.646 65.1534 1.17086
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Measured 23693.7 18263 1.29736
165 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Ranked 209.299 249.187 1.19058
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Squared 173408 242989 1.40126
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Rooted 55.6486 65.1478 1.1707
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Measured 23693.7 18263 1.29736
166 gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Ranked 209.299 249.187 1.19058
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Squared 173408 242989 1.40126
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Rooted 55.6495 65.1458 1.17064
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Measured 23693.7 18263 1.29736
167 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Ranked 209.299 249.187 1.19058
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Squared 173408 242989 1.40126
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Rooted 55.65 65.1448 1.17062
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Measured 23693.7 18263 1.29736
168 gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Ranked 82.5916 98.0548 1.18722
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Measured 23693.7 18263 1.29736
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Squared 173408 242989 1.40126
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Rooted 56.3709 65.8949 1.16895
169 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Ranked 82.5916 98.0548 1.18722
cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Rooted 62.762 53.7761 1.1671

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/