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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Filtered green Gene red Interaction Map network_comparison Value Type Network Comparison Type Rank description
Results: HTML CSV LaTeX Showing element 501 to 550 of 77072 in total
Filtered  : 0
green
red
Interaction Map
network_comparison
Value Type
Network Comparison Type
Rank
description
5.39669 1.22698 High confidence 4.16971 Squared Subtracted 420 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]
4.39835 Divided 52
Low confidence 4.16971 Subtracted 774
4.39835 Divided 56
33.64 High confidence 6.23345 42 nanos (fragment). [sptrembl;acc:q8wy41]
28.2433 Subtracted 358
5.42219 12.5892 2.32179 Divided 91 lats homolog 1. [refseq;acc:nm_004690]
92 sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
7.16701 Subtracted 400 lats homolog 1. [refseq;acc:nm_004690]
401 sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
Low confidence 2.32179 Divided 90 lats homolog 1. [refseq;acc:nm_004690]
91 sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
7.16701 Subtracted 761 lats homolog 1. [refseq;acc:nm_004690]
762 sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
5.56738 199.549 High confidence 35.8425 Measured Divided 11 serpin b12. [swissprot;acc:q96p63]
193.982 Subtracted 168
Low confidence 35.8425 Divided 10
193.982 Subtracted 280
5.56776 5.83095 0.26319 Rooted 768 adapter-related protein complex 2 alpha 1 subunit (alpha-adaptin a) (adaptor protein complex ap-2 alpha-1 subunit) (clathrin assembly protein complex 2 alpha-a large chain) (100 kda coated vesicle protein a) (plasma membrane adaptor ha2/ap2 adaptin alpha a subunit). [swissprot;acc:o95782]
1.04727 Divided 544
5.58446 23.0581 4.12898 Squared 61 laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942]
17.4736 Subtracted 732
5.66499 9.92134 High confidence 1.75134 Rooted Divided 43 40s ribosomal protein s26. [swissprot;acc:p02383]
4.25635 Subtracted 115
5.71669 199.249 34.8539 Measured Divided 12 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]
193.532 Subtracted 169
Low confidence 34.8539 Divided 11
193.532 Subtracted 281
5.76 0.0236686 High confidence 5.73633 Squared 407 succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]
243.36 Divided 21
5.80317 0.0279126 Low confidence 5.77526 Subtracted 766 fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344]
207.905 Divided 15
5.80678 9.84765 1.69589 Rooted 32 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]
33 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
34 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]
35 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
36 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
37 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
39 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
40 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
41 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
42 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
43 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
44 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
45 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
47 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
48 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]
4.04087 Subtracted 196 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]
197 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
198 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]

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/