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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1351 to 1400 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
676 deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Low confidence 202.698 197.124 1.02828
dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] High confidence 232.469 245.613 1.05654
677 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Low confidence 207.03 201.339 1.02827
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] High confidence 228.944 216.745 1.05628
678 cytochrome p450 3a4 (ec 1.14.13.67) (quinine 3-monooxygenase) (cypiiia4) (nifedipine oxidase) (nf-25) (p450-pcn1). [swissprot;acc:p08684] Low confidence 203.747 198.152 1.02824
sorting nexin 5. [swissprot;acc:q9y5x3] High confidence 208.482 220.175 1.05609
679 glioma-amplified sequence-41; numa binding protein 1. [refseq;acc:nm_006530] Low confidence 198.424 192.974 1.02824
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence 132.413 125.389 1.05602
680 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]
putative alpha-mannosidase c20orf31 precursor (ec 3.2.1.-). [swissprot;acc:q9bv94] Low confidence 196.228 190.844 1.02821
681 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] High confidence 132.413 125.389 1.05602
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Low confidence 206.115 200.462 1.0282
682 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 204.263 198.663 1.02819
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] High confidence 132.413 125.389 1.05602
683 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Low confidence 216.618 210.69 1.02814
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] High confidence 132.413 125.389 1.05602
684 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Low confidence 199.669 194.204 1.02814
685 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] High confidence 132.413 125.389 1.05602
tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] Low confidence 201.719 196.209 1.02808
686 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 132.413 125.389 1.05602
neurogenin 2 (fragment). [swissprot;acc:q9h2a3] Low confidence 216.554 210.642 1.02807
687 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] High confidence 132.413 125.389 1.05602
688 dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] 237.554 250.823 1.05586
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Low confidence 216.552 210.641 1.02806
689 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] High confidence 135.379 128.225 1.05579
690 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Low confidence 216.552 210.641 1.02806
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] High confidence 220.593 208.987 1.05553
691 atp-dependent helicase ddx8 (rna helicase hrh1) (deah-box protein 8). [swissprot;acc:q14562] Low confidence 201.663 196.158 1.02806
breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] High confidence 217.602 206.195 1.05532
692 cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253]
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Low confidence 203.897 198.337 1.02803
693 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] 205.207 199.613 1.02802
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] High confidence 222.554 234.847 1.05524
694 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Low confidence 216.501 210.602 1.02801
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] High confidence 241.907 229.35 1.05475
695 paxillin. [swissprot;acc:p49023] Low confidence 202.649 197.13 1.028
peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] High confidence 226.135 214.405 1.05471
696 interferon-related developmental regulator 1 (nerve growth factor- inducible protein pc4). [swissprot;acc:o00458] Low confidence 204.538 198.974 1.02796
sr rich protein. [refseq;acc:nm_032870] High confidence 225.293 213.64 1.05455
697 chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Low confidence 202.744 197.238 1.02792
ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] High confidence 220.444 209.113 1.05419
698 mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] 220.437 209.118 1.05413
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Low confidence 196.49 201.972 1.0279
699 adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382] 205.169 199.601
cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] High confidence 220.438 209.118 1.05413
700 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]
wd-repeat protein 6. [swissprot;acc:q9nnw5] Low confidence 204.863 199.304 1.02789

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/