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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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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1362 to 1411 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
Hugo
description
Interaction Map
red
green
network_comparison
681 HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] High confidence 132.413 125.389 1.05602
682 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
DDX54 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Low confidence 204.263 198.663 1.02819
683 CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] 216.618 210.69 1.02814
HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] High confidence 132.413 125.389 1.05602
684 no value repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Low confidence 199.669 194.204 1.02814
HOXB5 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] High confidence 132.413 125.389 1.05602
685 HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]
TDO2 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 no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 132.413 125.389 1.05602
NEUROG2 neurogenin 2 (fragment). [swissprot;acc:q9h2a3] Low confidence 216.554 210.642 1.02807
687 HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] High confidence 132.413 125.389 1.05602
NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Low confidence 216.554 210.642 1.02807
688 NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 216.552 210.641 1.02806
POLR2D dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] High confidence 237.554 250.823 1.05586
689 NEUROD1 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Low confidence 216.552 210.641 1.02806
TCP1 t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] High confidence 135.379 128.225 1.05579
690 NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Low confidence 216.552 210.641 1.02806
SNW1 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 BCAS2 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 217.602 206.195 1.05532
DHX8 atp-dependent helicase ddx8 (rna helicase hrh1) (deah-box protein 8). [swissprot;acc:q14562] Low confidence 201.663 196.158 1.02806
692 CDC5L 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] High confidence 217.602 206.195 1.05532
PPAN-P2RY11 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Low confidence 203.897 198.337 1.02803
693 no value 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
NOVA1 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 CDK2AP1 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
POLE 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 PPIL4 peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] 226.135 214.405 1.05471
PXN paxillin. [swissprot;acc:p49023] Low confidence 202.649 197.13 1.028
696 IFRD1 interferon-related developmental regulator 1 (nerve growth factor- inducible protein pc4). [swissprot;acc:o00458] 204.538 198.974 1.02796
SFRS18 sr rich protein. [refseq;acc:nm_032870] High confidence 225.293 213.64 1.05455
697 FTH1 ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] 220.444 209.113 1.05419
SUPT16H chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Low confidence 202.744 197.238 1.02792
698 FTMT mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] High confidence 220.437 209.118 1.05413
VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Low confidence 196.49 201.972 1.0279
699 AP1S1 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
CREG2 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] High confidence 220.438 209.118 1.05413
700 no value dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]
WDR6 wd-repeat protein 6. [swissprot;acc:q9nnw5] Low confidence 204.863 199.304 1.02789
701 ACO1 iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399] 200.577 195.136 1.02788
DLGAP1 disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] High confidence 220.438 209.118 1.05413
702 AHCYL1 putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865]
G3BP1 ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283] Low confidence 211.28 217.166 1.02786
703 KIAA0430 limkain b1. [refseq;acc:nm_019081] High confidence 220.438 209.118 1.05413
PWP1 periodic tryptophan protein 1 homolog (keratinocyte protein ief ssp 9502). [swissprot;acc:q13610] Low confidence 203.581 198.065 1.02785
704 no value putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] High confidence 220.438 209.118 1.05413
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Low confidence 204.411 198.876 1.02783
705 CREG1 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] High confidence 220.438 209.118 1.05413
SPATA5 spermatogenesis associated factor spaf. [refseq;acc:nm_145207] Low confidence 205.124 199.576 1.0278
706 DLGAP3 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] High confidence 220.438 209.118 1.05413

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
- Hugo is the HGNC identifier if it exists
- 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/