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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1964 to 2013 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
246 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Measured 1 4252.66 5213.05 1.22583
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Ranked 0 10551.6 11573.7 1.09687
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Measured 1225.09 1079.36 1.13502
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Rooted 12.8935 14.3151 1.11026
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 1 146.94 167.046 1.13683
247 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] Squared 0 20324.3 15893.2 1.2788
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 1 8875.01 6768.05 1.31131
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] Measured 0 1225.09 1079.36 1.13502
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Ranked 10551.6 11573.7 1.09687
neurocalcin delta. [swissprot;acc:p29554] Rooted 12.8769 11.6055 1.10955
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 1 47.3621 53.8355 1.13668
rna-binding protein. [refseq;acc:nm_019027] Ranked 237.302 212.41 1.11719
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Measured 6416.68 7865.15 1.22574
248 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Ranked 237.302 212.41 1.11719
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Rooted 0 30.7397 27.7265 1.10868
keratin associated protein 1.5. [refseq;acc:nm_031957] Ranked 10551.6 11573.7 1.09687
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Measured 1225.09 1079.37 1.135
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Squared 1 8875.01 6768.05 1.31131
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Measured 6417.18 7859.6 1.22477
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Rooted 56.0466 63.4808 1.13264
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Squared 0 42556.5 33335.4 1.27662
249 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 35446.2 27772 1.27633
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 1 8875.01 6768.05 1.31131
hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Rooted 0 23.5797 26.096 1.10671
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] Measured 1225.08 1079.37 1.135
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Ranked 10551.6 11573.7 1.09687
ns1-associated protein 1. [refseq;acc:nm_006372] 1 237.302 212.41 1.11719
transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Rooted 55.5965 62.9349 1.13199
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Measured 6417.18 7859.59 1.22477
250 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Squared 69201.8 53013.4 1.30536
dc11 protein. [refseq;acc:nm_020186] Rooted 0 23.5797 26.096 1.10671
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Squared 504.762 643.571 1.275
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Ranked 1 237.302 212.41 1.11719
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] 0 10551.6 11573.7 1.09687
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Measured 1225.08 1079.37 1.135
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Rooted 1 55.5965 62.9349 1.13199
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Measured 6417.18 7859.6 1.22477
251 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Rooted 0 21.3142 23.5833 1.10646
b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Squared 1 69165.6 52992.1 1.30521
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Ranked 0 10551.6 11573.6 1.09686
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Measured 1225.08 1079.38 1.13498
max protein. [swissprot;acc:p25912] Rooted 1 56.3054 63.7148 1.13159
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Ranked 186.172 166.661 1.11707
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Measured 6417.18 7859.6 1.22477
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Squared 0 25574.2 20063.8 1.27464
252 crk-like protein. [swissprot;acc:p46109] Measured 1 6417.18 7859.6 1.22477
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Ranked 237.292 212.457 1.11689
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 0 10551.6 11573.5 1.09685
lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] Rooted 21.1331 19.1063 1.10608
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] 1 51.6736 58.4422 1.13099

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/