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 813 to 862 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
102 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] Ranked 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
musashi 2 isoform a. [refseq;acc:nm_138962] Measured Divided 4241.57 5810.79 1.36996
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Rooted Subtracted 19.9625 35.798 15.8355
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Ranked 256.228 298.438 42.21
105 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Squared Divided 407289 263351 1.54656
fos-related antigen 2. [swissprot;acc:p15408] Rooted 60.8675 77.7168 1.27682
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Ranked 266.716 333.165 1.24914
musashi 1. [refseq;acc:nm_002442] Measured 4241.57 5810.79 1.36996
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Subtracted 11068 8508.5 2559.5
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Squared 90432.9 56304.2 34128.7
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Rooted 63.7477 48.1588 15.5889
transcription factor jun-d. [swissprot;acc:p17535] Ranked 200.941 158.941 42
106 cytohesin 4. [swissprot;acc:q9uia0] Squared Divided 407289 263351 1.54656
nostrin. [refseq;acc:nm_052946] Ranked Subtracted 209.299 249.187 39.888
nuclear protein ukp68. [refseq;acc:nm_024824] Measured Divided 4241.57 5810.79 1.36996
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Rooted 60.8692 77.7165 1.27678
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Measured Subtracted 11068 8508.5 2559.5
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] Squared 82624.3 115061 32436.7
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Ranked Divided 252.329 202.004 1.24913
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Rooted Subtracted 63.7477 48.1589 15.5888
107 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Measured Divided 4266.04 5843.51 1.36977
cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Squared 407289 263351 1.54656
eap30 subunit of ell complex. [refseq;acc:nm_007241] Ranked Subtracted 209.299 249.187 39.888
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Rooted Divided 60.875 77.7152 1.27664
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Ranked 252.309 201.998 1.24907
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Squared Subtracted 84857.8 53402.4 31455.4
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Measured 14229.2 16780.7 2551.5
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Rooted 63.7477 48.1594 15.5883
108 filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Measured Divided 4366.44 5899.76 1.35116
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Ranked 252.296 201.995 1.24902
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Subtracted 209.299 249.187 39.888
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Squared Divided 19321 12542.6 1.54043
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Measured Subtracted 14021.4 11523 2498.4
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Squared 78383 108483 30100

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/