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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 144 to 193 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
72 putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] 0 4119 5397 1.31027
73 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 288 362 1.25694
phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] 0 4119 5397 1.31027
74 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 6742.5 8759.5 1.29915
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 288 362 1.25694
75 nanos (fragment). [sptrembl;acc:q8wy41] 0 8782 11350 1.29242
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] 1 288 362 1.25694
76 db83 protein. [swissprot;acc:p57088]
spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] 0 3474 2695 1.28905
77 regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] 8821.32 11366.5 1.28853
voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 1 254.692 202.668 1.2567
78 repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 0 7584.72 9706.12 1.27969
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 1 254.693 202.668 1.2567
79 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 0 9465.55 12106.5 1.27901
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] 1 254.693 202.668 1.2567
80 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 0 9102.34 11617.9 1.27636
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 1 254.691 202.668 1.25669
81 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 0 14463 11356 1.2736
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 1 254.614 202.646 1.25645
82 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 0 7706.5 6058 1.27212
guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] 1 267.636 335.359 1.25304
83 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 88.2482 110.265 1.24949
small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678] 0 18359.8 14447.8 1.27077
84 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 1 88.2482 110.265 1.24949
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] 0 12460.6 15781 1.26647
85 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 1 88.2482 110.265 1.24949
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] 0 9688.47 12104.2 1.24934
86 high mobility group protein 1 (hmg-1). [swissprot;acc:p09429] 5677.96 4546.87 1.24876
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 1 88.2482 110.265 1.24949
87 dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4] 0 5677.89 4547.43 1.24859
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 1 88.2482 110.265 1.24949
88 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6] 0 5677.86 4547.66 1.24852
89 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 1 88.2482 110.265 1.24949
nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497] 0 5677.58 4549.85 1.24786
90 high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] 5677.45 4550.87 1.24755
necdin. [swissprot;acc:q99608] 1 88.2482 110.265 1.24949
91 bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] 0 13841.2 11127.5 1.24387
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 1 88.2482 110.265 1.24949
92 dok-like protein. [refseq;acc:nm_024872] 0 17571 21783 1.23971
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 1 88.2482 110.265 1.24949
93 melanoma antigen, family b, 6. [refseq;acc:nm_173523]
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] 0 7739.47 9580.95 1.23793
94 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 1 88.2482 110.265 1.24949
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] 0 12946.3 10519.7 1.23067
95 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 1 88.2482 110.265 1.24949
pp3111 protein. [refseq;acc:nm_022156] 0 6185 7603 1.22926
96 imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 8335.82 10228.3 1.22703
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 1 88.2482 110.265 1.24949
97 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]

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/