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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 801 to 850 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
101 CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Squared Divided 222655 143584 1.5507
CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Measured 2353.63 3225.65 1.3705
DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Rooted Subtracted 19.9625 35.798 15.8355
FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Ranked 204.641 161.051 43.59
GNAO1 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Rooted Divided 47.6504 36.9304 1.29028
MAGEB4 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
SEPT4 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 Subtracted 14924.4 17655.2 2730.8
SEPT6 septin 6. [swissprot;acc:q14141] Squared 88953.6 124854 35900.4
102 CLP1 pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] 121200 85473.4 35726.6
CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Rooted 19.9625 35.798 15.8355
FIP1L1 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Squared Divided 214143 138337 1.54798
FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Ranked Subtracted 204.642 161.068 43.574
MAGED2 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
PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Measured 2353.63 3225.65 1.3705
RAP1GAP rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Rooted 47.6504 36.9304 1.29028
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Measured Subtracted 11068 8508.5 2559.5
103 no value 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
CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Measured Subtracted 11068 8508.5 2559.5
CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Rooted 19.9625 35.798 15.8355
CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Measured Divided 2353.63 3225.65 1.3705
FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Rooted 60.8365 77.7233 1.27758
JUNB transcription factor jun-b. [swissprot;acc:p17275] Ranked Subtracted 201.144 158.868 42.276
SYMPK symplekin. [swissprot;acc:q92797] Squared 124118 88668.8 35449.2
TRO trophinin. [swissprot;acc:q12816] Ranked Divided 88.2482 110.265 1.24949
104 no value jun dimerization protein. [refseq;acc:nm_130469] Rooted 60.8365 77.7233 1.27758
CSTF2T likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Squared Subtracted 121579 87259.3 34319.7
HOMER2 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Ranked Divided 252.371 202.016 1.24926
MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Measured 4241.57 5810.79 1.36996
PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Squared 407289 263351 1.54656
RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Rooted Subtracted 19.9625 35.798 15.8355
STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Measured 11068 8508.5 2559.5
TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Ranked 256.228 298.438 42.21
105 no value 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
FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Divided 60.8675 77.7168 1.27682
GNB1 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
JUND transcription factor jun-d. [swissprot;acc:p17535] Subtracted 200.941 158.941 42
MSI1 musashi 1. [refseq;acc:nm_002442] Measured Divided 4241.57 5810.79 1.36996
PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Squared 407289 263351 1.54656
RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Subtracted 90432.9 56304.2 34128.7
VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Measured 11068 8508.5 2559.5
106 CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43]
COQ7 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
FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Rooted 60.8692 77.7165 1.27678
NOSTRIN nostrin. [refseq;acc:nm_052946] Ranked Subtracted 209.299 249.187 39.888
PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Rooted 63.7477 48.1589 15.5888
PSCD4 cytohesin 4. [swissprot;acc:q9uia0] Squared Divided 407289 263351 1.54656
SEPT4 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] Subtracted 82624.3 115061 32436.7
ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Measured Divided 4241.57 5810.79 1.36996
107 FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Rooted 60.875 77.7152 1.27664
HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Ranked 252.309 201.998 1.24907

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
- Hugo is the HGNC identifier if it exists
- 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/