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 [...,...].
Filtered green Gene Value Type red network_comparison Network Comparison Type Interaction Map Rank description
Results: HTML CSV LaTeX Showing element 551 to 600 of 77072 in total
Filtered  : 0
green
Value Type
red
network_comparison
Network Comparison Type
Interaction Map
Rank
description
5.80678 Rooted 9.84765 4.04087 Subtracted Low confidence 199 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
200 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
201 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
202 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
203 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
204 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
205 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
206 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
207 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
208 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
209 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
210 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]
5.80679 1.69589 Divided 38 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
46 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
4.04086 Subtracted 211 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
212 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
5.86733 Squared 8.27667 1.41064 Divided High confidence 206 small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]
2.40934 Subtracted 434
5.87091 Rooted 3.30572 1.77599 Divided 41 suppressor of actin 1. [refseq;acc:nm_014016]
2.56519 Subtracted 218
5.90479 4.72248 1.18231 351 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]
1.25036 Divided 119
5.90864 Squared 0.213018 5.69562 Subtracted 408 ptd016 protein. [refseq;acc:nm_016125]
Low confidence 767
27.7377 Divided High confidence 28
Low confidence 17
5.9911 11.4237 1.90678 114 protein tyrosine phosphatase type iva, member 2 isoform 1; protein tyrosine phosphatase iva2; protein tyrosine phosphatase iva; phosphatase of regenerating liver 2. [refseq;acc:nm_003479]
5.4326 Subtracted 768
6.06104 Rooted 7.7419 1.27732 Divided High confidence 110 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]
1.68086 Subtracted 299
6.08276 8.12404 1.33558 Divided Low confidence 87 arf gtpase-activating protein. [refseq;acc:nm_133446]
88 up-regulated in liver cancer 1; similar to development- and differentiation-enhancing factor 2. [refseq;acc:nm_017707]
2.04128 Subtracted 365 arf gtpase-activating protein. [refseq;acc:nm_133446]
366 up-regulated in liver cancer 1; similar to development- and differentiation-enhancing factor 2. [refseq;acc:nm_017707]
6.15501 Squared 21.2079 3.44563 Divided High confidence 62 elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]
15.0529 Subtracted 386
6.23127 Rooted 4.28588 1.45391 Divided 59 metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]
Low confidence 62
1.94539 Subtracted High confidence 281
Low confidence 375
6.30196 6.24948 0.05248 High confidence 486 adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]
1.0084 Divided 478
6.32456 6.55744 0.23288 Subtracted Low confidence 776 probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1]
1.03682 Divided 589
6.488 8.14325 1.25512 112 sarcoplasmic/endoplasmic reticulum calcium atpase 1 (ec 3.6.3.8) (calcium pump 1) (serca1) (sr ca(2+)-atpase 1) (calcium-transporting atpase sarcoplasmic reticulum type, fast twitch skeletal muscle isoform) (endoplasmic reticulum class 1/2 ca(2+) atpase). [swissprot;acc:o14983]
1.65525 Subtracted 436
6.50325 Measured 130.512 20.0687 Divided High confidence 14 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]
124.009 Subtracted 258
6.55744 Rooted 0 6.55744 65 sedlin. [swissprot;acc:o14582]
66 synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]

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/