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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 780 to 829 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
98 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Measured Divided 2353.63 3225.65 1.3705
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Ranked Subtracted 204.641 160.957 43.684
septin 10 isoform 1. [refseq;acc:nm_144710] Squared 89578.7 125883 36304.3
transcription factor lbx1. [swissprot;acc:p52954] Rooted Divided 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
jun dimerization protein. [refseq;acc:nm_130469] Ranked 204.641 160.957 43.684
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Divided 88.2482 110.265 1.24949
mosaic protein lgn. [swissprot;acc:p81274] Rooted 47.6504 36.9304 1.29028
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 2353.63 3225.65 1.3705
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Subtracted 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] Squared Divided 226186 145568 1.55382
100 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
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] Measured 2353.63 3225.65 1.3705
fos-related antigen 2. [swissprot;acc:p15408] Ranked Subtracted 204.641 161.046 43.595
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Divided 88.2482 110.265 1.24949
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Rooted 47.6504 36.9304 1.29028
septin 6. [swissprot;acc:q14141] Measured Subtracted 15959.9 18957.1 2997.2
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Squared 89182.8 125229 36046.2
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Rooted 19.9625 35.798 15.8355
101 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Squared Divided 222655 143584 1.5507
cullin homolog 2 (cul-2). [swissprot;acc:q13617] Measured 2353.63 3225.65 1.3705
dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Rooted Subtracted 19.9625 35.798 15.8355
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Divided 47.6504 36.9304 1.29028
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Ranked 88.2482 110.265 1.24949
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Subtracted 204.641 161.051 43.59
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Measured 14924.4 17655.2 2730.8
septin 6. [swissprot;acc:q14141] Squared 88953.6 124854 35900.4
102 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Measured 11068 8508.5 2559.5
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Rooted 19.9625 35.798 15.8355
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Squared Divided 214143 138337 1.54798
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Ranked Subtracted 204.642 161.068 43.574
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Divided 88.2482 110.265 1.24949
pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] Squared Subtracted 121200 85473.4 35726.6
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Measured Divided 2353.63 3225.65 1.3705
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Rooted 47.6504 36.9304 1.29028
103 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Measured 2353.63 3225.65 1.3705
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Rooted Subtracted 19.9625 35.798 15.8355
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] Squared Divided 407289 263351 1.54656
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Rooted 60.8365 77.7233 1.27758
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Measured Subtracted 11068 8508.5 2559.5
symplekin. [swissprot;acc:q92797] Squared 124118 88668.8 35449.2
transcription factor jun-b. [swissprot;acc:p17275] Ranked 201.144 158.868 42.276
trophinin. [swissprot;acc:q12816] Divided 88.2482 110.265 1.24949
104 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Measured Subtracted 11068 8508.5 2559.5
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Squared Divided 407289 263351 1.54656
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Ranked 252.371 202.016 1.24926
jun dimerization protein. [refseq;acc:nm_130469] Rooted 60.8365 77.7233 1.27758
likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Squared Subtracted 121579 87259.3 34319.7

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/