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 1012 to 1061 of 66312 in total
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
Interaction Map
red
network_comparison
green
64 FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Subtracted Ranked Low confidence 202.793 19.832 182.961
GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Divided Rooted High confidence 63.8686 1.35128 47.2654
GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Ranked 266.868 1.25965 336.159
HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Measured Low confidence 15464.1 1.13635 17572.7
JUND transcription factor jun-d. [swissprot;acc:p17535] Ranked 202.709 1.10552 183.361
MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Subtracted Rooted High confidence 137.446 16.623 120.823
MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] Divided Squared 219048 1.68808 129762
NCDN neurochondrin. [refseq;acc:nm_014284] Low confidence 73677.6 1.28138 57498.7
NFYA ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Subtracted Ranked High confidence 260.532 56.223 204.309
PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided Measured 4489.19 1.6231 2765.82
RAB11FIP4 rab11-family interacting protein 4. [refseq;acc:nm_032932] Rooted Low confidence 73.6221 1.10693 81.4944
RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Subtracted Measured 10585.5 1053.1 11638.6
SEPT7 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Squared 66860.1 13713.3 80573.4
65 no value melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Divided High confidence 219048 1.68808 129762
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] Subtracted Ranked 187.457 56.221 243.678
BRAP brca1 associated protein. [refseq;acc:nm_006768] Squared Low confidence 83524.5 13703.3 69821.2
CSTF3 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Measured High confidence 22515.5 3812.9 18702.6
FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Ranked Low confidence 202.792 19.818 182.974
GNAQ guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Divided High confidence 267.136 1.25807 336.077
JMJD1C thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Subtracted Measured Low confidence 1917.64 1032.86 2950.5
JUNB transcription factor jun-b. [swissprot;acc:p17275] Divided Ranked 202.728 1.10546 183.388
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] Subtracted Rooted High confidence 137.446 16.623 120.823
MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Squared 144912 63757 81155
NEURL neuralized-like. [refseq;acc:nm_004210] Divided Measured 1657.68 1.6229 2690.25
PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Rooted 63.8686 1.35128 47.2654
RAB11FIP3 eferin. [swissprot;acc:o75154] Low confidence 73.6221 1.10693 81.4944
SEPT6 septin 6. [swissprot;acc:q14141] Measured 13005.8 1.13593 14773.7
SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Squared 75490.8 1.26497 95493.3
XKR7 dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Subtracted Rooted 75.1927 7.3584 82.5511
66 ARAF a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Measured High confidence 17757.5 3749.5 14008
DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Divided Rooted Low confidence 55.8923 1.10573 61.8016
FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Subtracted Ranked 202.79 19.773 183.017
GNA11 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Divided High confidence 267.136 1.25807 336.077
GNPDA2 glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] Subtracted Rooted Low confidence 52.3425 7.2858 45.0567
MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Divided Squared High confidence 219048 1.68808 129762
MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Subtracted 144911 63756.3 81154.7
MTUS1 mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Divided Ranked Low confidence 221.902 1.10518 200.783
NDUFA12 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Measured High confidence 1991.03 1.61795 3221.38
NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Subtracted Squared Low confidence 60583.7 13696.3 74280
PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Ranked High confidence 187.458 56.22 243.678
PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Divided Rooted 63.8686 1.35128 47.2654
SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] Squared Low confidence 74803.9 1.26038 94281
SON son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Measured 4900.7 1.13368 5555.81
TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Subtracted 1921.96 1032.28 2954.24
TRO trophinin. [swissprot;acc:q12816] Rooted High confidence 137.446 16.623 120.823
67 AHCYL1 putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Ranked Low confidence 195.817 19.699 215.516
ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Divided Measured High confidence 6475.5 1.59177 10307.5
ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted Squared 144876 63739.5 81136.5
GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Rooted 63.8686 16.6032 47.2654
GNAT2 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Divided Ranked 267.14 1.25805 336.075

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/