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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 801 to 850 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
red
network_comparison
green
101 CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Divided Squared 222655 1.5507 143584
CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Measured 2353.63 1.3705 3225.65
DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Subtracted Rooted 19.9625 15.8355 35.798
FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Ranked 204.641 43.59 161.051
GNAO1 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Divided Rooted 47.6504 1.29028 36.9304
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 1.24949 110.265
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 Measured 14924.4 2730.8 17655.2
SEPT6 septin 6. [swissprot;acc:q14141] Squared 88953.6 35900.4 124854
102 CLP1 pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] 121200 35726.6 85473.4
CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Rooted 19.9625 15.8355 35.798
FIP1L1 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Divided Squared 214143 1.54798 138337
FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Subtracted Ranked 204.642 43.574 161.068
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 1.24949 110.265
PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Measured 2353.63 1.3705 3225.65
RAP1GAP rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Rooted 47.6504 1.29028 36.9304
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Subtracted Measured 11068 2559.5 8508.5
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] Divided Squared 407289 1.54656 263351
CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Subtracted Measured 11068 2559.5 8508.5
CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Rooted 19.9625 15.8355 35.798
CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Divided Measured 2353.63 1.3705 3225.65
FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Rooted 60.8365 1.27758 77.7233
JUNB transcription factor jun-b. [swissprot;acc:p17275] Subtracted Ranked 201.144 42.276 158.868
SYMPK symplekin. [swissprot;acc:q92797] Squared 124118 35449.2 88668.8
TRO trophinin. [swissprot;acc:q12816] Divided Ranked 88.2482 1.24949 110.265
104 no value jun dimerization protein. [refseq;acc:nm_130469] Rooted 60.8365 1.27758 77.7233
CSTF2T likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Subtracted Squared 121579 34319.7 87259.3
HOMER2 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Divided Ranked 252.371 1.24926 202.016
MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Measured 4241.57 1.36996 5810.79
PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Squared 407289 1.54656 263351
RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Subtracted Rooted 19.9625 15.8355 35.798
STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Measured 11068 2559.5 8508.5
TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Ranked 256.228 42.21 298.438
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 15.5889 48.1588
FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Divided 60.8675 1.27682 77.7168
GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Ranked 266.716 1.24914 333.165
JUND transcription factor jun-d. [swissprot;acc:p17535] Subtracted 200.941 42 158.941
MSI1 musashi 1. [refseq;acc:nm_002442] Divided Measured 4241.57 1.36996 5810.79
PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Squared 407289 1.54656 263351
RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Subtracted 90432.9 34128.7 56304.2
VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Measured 11068 2559.5 8508.5
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] Divided Ranked 252.329 1.24913 202.004
FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Rooted 60.8692 1.27678 77.7165
NOSTRIN nostrin. [refseq;acc:nm_052946] Subtracted Ranked 209.299 39.888 249.187
PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Rooted 63.7477 15.5888 48.1589
PSCD4 cytohesin 4. [swissprot;acc:q9uia0] Divided Squared 407289 1.54656 263351
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 32436.7 115061
ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Divided Measured 4241.57 1.36996 5810.79
107 FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Rooted 60.875 1.27664 77.7152
HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Ranked 252.309 1.24907 201.998

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/