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 Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1651 to 1700 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
red
network_comparison
green
207 CLSTN2 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Subtracted Measured 10600.3 1464.9 12065.2
CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Rooted 136.706 10.141 126.565
EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Ranked 237.312 24.949 212.363
PEX19 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Squared 46739.9 12394.6 59134.5
PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Divided Ranked 285.684 1.13261 252.234
SLC4A1AP solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] Squared 70525.9 1.33879 52678.7
208 no value 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Subtracted Ranked 240.782 24.935 265.717
BHLHB4 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Squared 62783.5 11999.4 50784.1
CACNG8 voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Divided Measured 4068.78 1.24907 5082.18
CKS2 cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Squared 70525.9 1.33879 52678.7
CLSTN3 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Subtracted Measured 10599.9 1464.8 12064.7
DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Divided Rooted 46.901 1.14334 53.624
SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] Subtracted 113.733 10.138 123.871
SKP1A s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Divided Ranked 285.684 1.13261 252.234
209 no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted Rooted 121.695 10.12 131.815
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Measured 11383.2 1456.59 9926.61
BCCIP brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] Ranked 240.782 24.935 265.717
BHLHB5 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Squared 62757.7 11989.9 50767.8
CACNG3 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Divided Measured 4068.78 1.24907 5082.18
CAPN2 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Rooted 46.8525 1.14257 53.5324
CTNNAL1 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Squared 70525.9 1.33879 52678.7
FBXW7 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Ranked 285.684 1.13261 252.234
210 no value rna-binding protein. [refseq;acc:nm_019027] Subtracted 237.302 24.892 212.41
ATG5 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] Squared 36359.2 11892.4 24466.8
CACNG2 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Divided Measured 4068.82 1.24906 5082.21
CAPN1 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Rooted 46.8525 1.14256 53.5316
CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Ranked 285.684 1.13261 252.234
HOXB4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Subtracted Rooted 121.695 10.12 131.815
LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Measured 4355.61 1455.21 5810.82
SGTA small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Divided Squared 69549 1.33652 92953.5
211 no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Subtracted Ranked 237.302 24.892 212.41
CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Divided Measured 4068.91 1.24905 5082.27
HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Subtracted Rooted 121.695 10.12 131.815
LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Measured 4358.13 1453.36 5811.49
PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Divided Rooted 88.4361 1.14095 77.5112
PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Ranked 285.684 1.13261 252.234
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Subtracted Squared 28994.2 11859.4 17134.8
TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Divided 14668.3 1.3326 19547
212 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted Rooted 121.695 10.12 131.815
ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Divided 88.4266 1.14092 77.5047
BRF1 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] Measured 4446.72 1.24896 5553.79
CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Subtracted Squared 28994.2 11859.4 17134.8
CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Divided Ranked 285.684 1.13261 252.234
SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Subtracted 237.302 24.892 212.41
TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Divided Squared 14690.3 1.3315 19560.2
WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Subtracted Measured 6416.68 1448.47 7865.15
213 CPA6 carboxypeptidase b precursor. [refseq;acc:nm_020361] 7711.38 1445.58 6265.8
HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Ranked 237.302 24.892 212.41
HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Rooted 121.695 10.12 131.815
NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Divided Measured 4446.72 1.24896 5553.79

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/