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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3101 to 3150 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1551 adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235] Divided 225.159 221.424 1.01687
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Subtracted 221.128 224.767 3.639
1552 adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141] Divided 225.159 221.424 1.01687
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Subtracted 221.128 224.767 3.639
1553 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] Divided 215.389 211.833 1.01679
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] Subtracted 221.128 224.767 3.639
1554 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] Divided 196.215 193.018 1.01656
eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262] Subtracted 221.128 224.767 3.639
1555 pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Divided 196.192 192.996 1.01656
putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Subtracted 221.128 224.767 3.639
1556 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Divided 196.192 192.996 1.01656
valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] Subtracted 223.589 227.219 3.63
1557 adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567] 222.166 225.79 3.624
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Divided 196.192 192.996 1.01656
1558 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 196.171 192.977 1.01655
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Subtracted 115.817 119.432 3.615
1559 b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Divided 196.191 192.996 1.01655
tata element modulatory factor (tmf). [swissprot;acc:p82094] Subtracted 222.585 218.982 3.603
1560 p66 alpha. [refseq;acc:nm_017660] Divided 167.687 170.455 1.01651
scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680] Subtracted 222.585 218.982 3.603
1561 nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948]
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Divided 167.687 170.455 1.01651
1562 ammecr1 protein. [refseq;acc:nm_015365] Subtracted 222.585 218.982 3.603
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Divided 167.687 170.455 1.01651
1563 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] 218.277 214.739 1.01648
mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] Subtracted 222.585 218.982 3.603
1564 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] 222.133 225.731 3.598
atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] Divided 218.277 214.739 1.01648
1565 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] Subtracted 222.134 225.731 3.597
eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5] Divided 221.128 224.767 1.01646
1566 adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [swissprot;acc:o43747] Subtracted 222.134 225.731 3.597
erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584] Divided 221.128 224.767 1.01646
1567 adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3] Subtracted 222.134 225.731 3.597
bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] Divided 221.128 224.767 1.01646
1568 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] Subtracted 222.134 225.731 3.597
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Divided 221.128 224.767 1.01646
1569 glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Subtracted 159.75 156.153 3.597
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Divided 221.128 224.767 1.01646
1570 endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Subtracted 159.86 156.275 3.585
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] Divided 221.128 224.767 1.01646
1571 eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262]
trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] Subtracted 213.546 209.965 3.581
1572 gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]
putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Divided 221.128 224.767 1.01646
1573 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Subtracted 121.428 125.004 3.576
r3h domain protein 1. [swissprot;acc:q15032] Divided 218.105 214.573 1.01646
1574 glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Subtracted 159.993 156.421 3.572
tata element modulatory factor (tmf). [swissprot;acc:p82094] Divided 222.585 218.982 1.01645
1575 adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [swissprot;acc:p21851] Subtracted 222.103 225.675 3.572
scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680] Divided 222.585 218.982 1.01645

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/