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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank description red Value Type Network Comparison Type Interaction Map network_comparison Filtered green
Results: HTML CSV LaTeX Showing element 501 to 550 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
red
Value Type
Network Comparison Type
network_comparison
green
63 myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 4489.19 Measured Divided 1.6231 2765.82
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] 260.532 Ranked Subtracted 56.223 204.309
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] 189976 Squared 65496 124480
spermatogenesis associated 6. [refseq;acc:nm_019073] 6475.5 Measured 3832 10307.5
64 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 63.8686 Rooted Divided 1.35128 47.2654
amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 6475.5 Measured Subtracted 3832 10307.5
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] 260.532 Ranked 56.223 204.309
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 144940 Squared 63770.3 81169.7
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 4489.19 Measured Divided 1.6231 2765.82
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 266.868 Ranked 1.25965 336.159
melanoma antigen, family b, 6. [refseq;acc:nm_173523] 219048 Squared 1.68808 129762
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 137.446 Rooted Subtracted 16.623 120.823
65 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 22515.5 Measured 3812.9 18702.6
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 63.8686 Rooted Divided 1.35128 47.2654
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 267.136 Ranked 1.25807 336.077
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 219048 Squared 1.68808 129762
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] 137.446 Rooted Subtracted 16.623 120.823
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 144912 Squared 63757 81155
neuralized-like. [refseq;acc:nm_004210] 1657.68 Measured Divided 1.6229 2690.25
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] 187.457 Ranked Subtracted 56.221 243.678
66 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 17757.5 Measured 3749.5 14008
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 63.8686 Rooted Divided 1.35128 47.2654
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 267.136 Ranked 1.25807 336.077
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 219048 Squared 1.68808 129762
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 144911 Subtracted 63756.3 81154.7
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] 1991.03 Measured Divided 1.61795 3221.38
trophinin. [swissprot;acc:q12816] 137.446 Rooted Subtracted 16.623 120.823
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 187.458 Ranked 56.22 243.678
67 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 63.8686 Rooted 16.6032 47.2654
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 6475.5 Measured Divided 1.59177 10307.5
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 144876 Squared Subtracted 63739.5 81136.5
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] 267.14 Ranked Divided 1.25805 336.075
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 219048 Squared 1.68808 129762
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 63.8686 Rooted 1.35128 47.2654
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] 17756.5 Measured Subtracted 3749.2 14007.3
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] 187.458 Ranked 56.219 243.677
68 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 6475.5 Measured Divided 1.59177 10307.5
cyclin g2. [swissprot;acc:q16589] 17738.6 Subtracted 3742.9 13995.7
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 139741 Squared 61286.4 78454.6
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 63.8686 Rooted 16.6032 47.2654
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided 1.35128
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 267.139 Ranked 1.25805 336.075
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 219048 Squared 1.68808 129762
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] 187.462 Ranked Subtracted 56.211 243.673
69 cyclin g1 (cyclin g). [swissprot;acc:p51959] 17738.5 Measured 3742.9 13995.6
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 63.8686 Rooted 16.6032 47.2654
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 267.14 Ranked Divided 1.25805 336.075
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 219048 Squared 1.68808 129762
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] 284.753 Ranked Subtracted 55.819 228.934
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] 27.9136 Rooted Divided 1.33581 37.2872

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/