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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1268 to 1317 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
159 necdin. [swissprot;acc:q99608] Measured Divided 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
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Rooted Subtracted 113.983 101.979 12.004
160 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Divided 52.7642 61.9019 1.17318
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Measured Subtracted 9035 7279.6 1755.4
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Ranked Divided 249.663 298.263 1.19466
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Squared 173408 242989 1.40126
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Rooted Subtracted 43.4291 31.7159 11.7132
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Measured Divided 23693.7 18263 1.29736
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Ranked Subtracted 312 284 28
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Squared 42788.3 60162.6 17374.3
161 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Divided 173408 242989 1.40126
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Measured 23693.7 18263 1.29736
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Subtracted 9035 7279.6 1755.4
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Ranked 312 284 28
ns1-associated protein 1. [refseq;acc:nm_006372] Rooted Divided 52.7642 61.9019 1.17318
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Subtracted 43.4519 31.7522 11.6997
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Ranked Divided 249.663 298.263 1.19466
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Squared Subtracted 52591.3 69845.1 17253.8
162 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Ranked 142 170 28
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Rooted Divided 52.7642 61.9019 1.17318
high-mobility group 20a. [refseq;acc:nm_018200] Measured Subtracted 5140.14 6893.53 1753.39
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Squared Divided 173408 242989 1.40126
kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Rooted Subtracted 43.4554 31.7576 11.6978
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Measured Divided 23693.7 18263 1.29736
nostrin. [refseq;acc:nm_052946] Ranked 209.299 249.187 1.19058
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Squared Subtracted 59704 76460.4 16756.4
163 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Rooted 54.935 66.6101 11.6751
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Ranked 133 105 28
c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Squared 59464 76120.8 16656.8
eap30 subunit of ell complex. [refseq;acc:nm_007241] Ranked Divided 209.299 249.187 1.19058
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
likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Measured Subtracted 14976.4 13246.6 1729.8
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Divided 23693.7 18263 1.29736
164 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Subtracted 4489.19 2765.82 1723.37
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Ranked 133 105 28
deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Squared 61733.5 45224.1 16509.4
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Divided 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
musashi 2 isoform a. [refseq;acc:nm_138962] Rooted Subtracted 54.9787 66.2416 11.2629
165 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Ranked Divided 209.299 249.187 1.19058
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Measured Subtracted 4489.19 2765.82 1723.37
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Squared Divided 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

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/