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.


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 Value Type Gene Network Comparison Type Rank Interaction Map network_comparison red description
Results: HTML CSV LaTeX Showing element 601 to 650 of 77072 in total
Filtered  : 0
green
Value Type
Network Comparison Type
Rank
Interaction Map
network_comparison
red
description
6.55744 Rooted Divided 145 High confidence 1.17775 5.56776 methyltransferase like 2. [refseq;acc:nm_018396]
Subtracted 65 6.55744 0 sedlin. [swissprot;acc:o14582]
66 synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
378 0.98968 5.56776 methyltransferase like 2. [refseq;acc:nm_018396]
6.80523 Divided 74 1.35766 5.01247 high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]
75 sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]
Subtracted 291 1.79276 high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]
292 sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]
6.85565 Divided 21 5.38516 36.9188 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]
29 Low confidence 1.7443 11.9583 glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]
44 High confidence
Subtracted 3 30.0631 36.9188 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]
62 Low confidence 5.10265 11.9583 glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]
91 High confidence
6.91035 Squared Divided 216 1.38378 9.56237 high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]
217 sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]
Subtracted 430 2.65202 high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]
431 sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]
6.95259 Rooted Divided 110 Low confidence 1.26588 8.80111 blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]
111 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]
Subtracted 385 1.84852 blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]
386 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]
6.95553 Divided 109 1.26597 8.80551
Subtracted 384 1.84998
6.96286 Divided 50 High confidence 1.58452 11.0328 importin 7; ran-binding protein 7. [refseq;acc:nm_006391]
Subtracted 126 4.06994
6.96791 Divided 114 Low confidence 1.25192 8.7233 laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942]
Subtracted 401 1.75539
6.97663 Divided 38 High confidence 1.92709 3.62029 spir-2 protein (fragment). [sptrembl;acc:q8wwl2]
Subtracted 157 3.35634
7.07107 Divided 100 Low confidence 1.29099 5.47723 transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]
106 High confidence
Subtracted 307 1.59384
444 Low confidence
7.14143 Divided 407 High confidence 1.03078 6.9282 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]
408 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
409 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]
410 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
411 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
412 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
413 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
414 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
415 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
416 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
417 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
418 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
419 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
420 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
421 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
422 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]

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/