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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Gene Rank description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1551 to 1600 of 66312 in total
Filtered  : 1
Rank
description
Network Comparison Type
Value Type
Interaction Map
red
green
network_comparison
97 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Divided Rooted Low confidence 68.5063 74.6906 1.09027
septin 10 isoform 1. [refseq;acc:nm_144710] Subtracted Measured High confidence 16067.4 19094.4 3027
98 brain protein 44. [swissprot;acc:o95563] 15999.1 19007.1 3008
cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] Squared Low confidence 57471.1 48463.4 9007.7
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Measured 12376.5 11436.5 940
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Divided Rooted 173.58 189.17 1.08981
guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Subtracted High confidence 40.2797 24.3705 15.9092
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Divided Ranked 88.2482 110.265 1.24949
mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Subtracted Rooted Low confidence 63.1259 69.4305 6.3046
phd finger protein 12; phd zinc finger transcription factor. [refseq;acc:nm_020889] Divided Squared 61253.4 51977.8 1.17845
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Measured High confidence 2353.63 3225.65 1.3705
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Subtracted Ranked 204.641 160.957 43.684
septin 10 isoform 1. [refseq;acc:nm_144710] Squared 89578.7 125883 36304.3
solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Divided Ranked Low confidence 200.497 185.679 1.0798
Subtracted 14.818
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Divided Measured 7624.8 8391.85 1.1006
transcription factor lbx1. [swissprot;acc:p52954] Rooted High confidence 47.6504 36.9304 1.29028
trs85 homolog. [swissprot;acc:q9y2l5] Squared 227160 146079 1.55505
99 brain protein 44. [swissprot;acc:o95563] Subtracted 89182.8 125229 36046.2
cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Divided Measured Low confidence 5752.65 6330.03 1.10037
eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] Ranked 200.497 185.679 1.0798
Subtracted 14.818
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Rooted 96.9641 103.242 6.2779
jun dimerization protein. [refseq;acc:nm_130469] Ranked High confidence 204.641 160.957 43.684
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Measured Low confidence 12376.4 11436.5 939.9
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Divided Ranked High confidence 88.2482 110.265 1.24949
mosaic protein lgn. [swissprot;acc:p81274] Rooted 47.6504 36.9304 1.29028
ras-related protein rab-37. [swissprot;acc:q96ax2] Squared Low confidence 61163.4 51924 1.17794
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] Measured High confidence 2353.63 3225.65 1.3705
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Rooted Low confidence 68.5805 74.7056 1.08931
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Subtracted Squared 59884.7 68850.8 8966.1
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Measured High confidence 15999.1 19007.1 3008
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Rooted 19.9625 35.798 15.8355
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Divided Squared 226186 145568 1.55382
100 b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] Ranked Low confidence 200.497 185.679 1.0798
Subtracted 14.818
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Divided Squared High confidence 226186 145568 1.55382
cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Subtracted Measured Low confidence 12375.5 11435.8 939.7
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] Divided High confidence 2353.63 3225.65 1.3705
fos-related antigen 2. [swissprot;acc:p15408] Subtracted Ranked 204.641 161.046 43.595
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Divided 88.2482 110.265 1.24949
monocarboxylate transporter 8 (mct 8) (x-linked pest-containing transporter) (mct 7). [swissprot;acc:p36021] Subtracted Squared Low confidence 63904 72791.6 8887.6
natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Divided Rooted 63.7749 69.4515 1.08901
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] High confidence 47.6504 36.9304 1.29028
septin 6. [swissprot;acc:q14141] Subtracted Measured 15959.9 18957.1 2997.2
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Squared 89182.8 125229 36046.2
set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] Divided Measured Low confidence 5752.65 6330.03 1.10037
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Subtracted Rooted High confidence 19.9625 35.798 15.8355
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Low confidence 61.9982 68.2337 6.2355
tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881] Divided Squared 70019.5 82296.2 1.17533

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/