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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 278 to 327 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
70 AMPD2 Measured amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 6475.5 10307.5 1.59177
CHD3 Rooted chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] 27.9136 37.2872 1.33581
GNAI2 Ranked guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] 267.142 336.074 1.25804
71 no value Measured 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] 4556.78 2945.26 1.54716
CDK2AP2 Rooted doc-1 related protein (doc-1r). [swissprot;acc:o75956] 27.9136 37.2872 1.33581
GNAI1 Ranked guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] 267.144 336.073 1.25802
MAGEA10 Squared melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 219048 129762 1.68808
72 GNAI3 Ranked guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] 267.144 336.073 1.25802
MAGEB4 Squared melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 219048 129762 1.68808
NEUROD6 Rooted neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 27.9136 37.2872 1.33581
PPP2R2D Measured uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 4556.79 2945.28 1.54715
73 JPH3 Ranked junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 288 362 1.25694
MAGED2 Squared 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] 219048 129762 1.68808
NEUROD1 Rooted neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 27.9136 37.2872 1.33581
PPP2R2B Measured 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] 4556.83 2945.38 1.54711
74 JPH2 Ranked junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 288 362 1.25694
NEUROD4 Rooted neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 27.9136 37.2872 1.33581
PPP2R2C Measured 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] 4556.99 2945.8 1.54694
TRO Squared trophinin. [swissprot;acc:q12816] 219048 129762 1.68808
75 CHD5 Rooted chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 27.9136 37.2872 1.33581
MYO5B Squared myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] 110342 184298 1.67024
NDUFS4 Measured nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] 1920.75 2907.43 1.5137
SMPD2 Ranked sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] 288 362 1.25694
76 CDK2AP1 Rooted cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] 27.9136 37.2872 1.33581
MYO5C Squared myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 110342 184298 1.67024
PPP2R1B Measured serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] 4599.26 3058.57 1.50373
TMEM33 Ranked db83 protein. [swissprot;acc:p57088] 288 362 1.25694
77 no value Squared myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 110342 184298 1.67024
CACNG2 Ranked voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 254.692 202.668 1.2567
PPP2R1A Measured serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] 4612.39 3093.6 1.49095
UNC84A Rooted sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 39.9725 52.9973 1.32584
78 ARAF Squared a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 117858 70570.1 1.67008
ATF3 Measured cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 4800.81 7132.71 1.48573
CACNG8 Ranked voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 254.693 202.668 1.2567
PPP2R2D Rooted uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 63.7477 48.1589 1.3237
79 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] 48.1588
CACNG3 Ranked voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] 254.693 202.668 1.2567
RAF1 Squared raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] 117850 70566.8 1.67005
UFC1 Measured protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 3074.57 4567.51 1.48558
80 CACNG4 Ranked voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 254.691 202.668 1.25669
PPP2R2B Rooted 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] 63.7477 48.1594 1.32368
PPP2R5E Squared serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] 117718 70505.9 1.66962
TIA1 Measured nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 4133.47 5945.32 1.43834
81 CACNG5 Ranked voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 254.614 202.646 1.25645
CCNG2 Squared cyclin g2. [swissprot;acc:q16589] 117718 70505.9 1.66962
PPP2R2C Rooted 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] 63.7475 48.1615 1.32362
TIAL1 Measured nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 4136.36 5943.56 1.43691
82 ATF3 Rooted cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 60.8022 79.5099 1.30768
CCNG1 Squared cyclin g1 (cyclin g). [swissprot;acc:p51959] 117718 70505.8 1.66962
GNB5 Ranked guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] 267.636 335.359 1.25304

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/