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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


Navigation/Query Panel:
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measured Rank Gene description expected Hugo final
Results: HTML CSV LaTeX Showing element 1458 to 1507 of 3206 in total
measured
Rank
description
expected
Hugo
final
0.104222 385 "DYNEIN INTERMEDIATE CHAIN 1, CYTOSOLIC (DH IC-1) (CYTOPLASMIC DYNEIN INTERMEDIATE CHAIN 1). [SWISSPROT;Acc:O14576]" 0.373698 DYNC1I1 0.278893652
0.104281 2043 HUNTINGTIN INTERACTING PROTEIN 1 (HIP-I). [SWISSPROT;Acc:O00291] 0.453153 HIP1 0.230123159
0.10445 2301 P10-BINDING PROTEIN. [RefSeq;Acc:NM_024491] 0.469849 CEP70 0.222305464
0.104453 667 SQV-7-LIKE PROTEIN (FRAGMENT). [SPTREMBL;Acc:O95454] 0.391317 SLC35D2 0.266926814
0.104678 2913 CYTOSKELETON RELATED VITAMIN A RESPONSIVE PROTEIN; GLUTAMATE TRANSPORTER EEAC1-ASSOCIATED PROTEIN; DERMAL PAPILLA DERIVED PROTEIN 11; PUTATIVE MAPK ACTIVATING PROTEIN PM27. [RefSeq;Acc:NM_006407] 0.601977 ARL6IP5 0.173890365
0.1052 346 DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1B (EC 2.7.1.-) (MIRK PROTEIN KINASE). [SWISSPROT;Acc:Q9Y463] 0.372425 DYRK1B 0.282472981
0.105213 716 P28 ING5. [RefSeq;Acc:NM_032329] 0.397328 ING5 0.264801373
0.105333 673 0.394979 SFT2D3 0.266680001
0.105382 1525 KINESIN-LIKE PROTEIN KIF3B (MICROTUBULE PLUS END-DIRECTED KINESIN MOTOR 3B) (HH0048). [SWISSPROT;Acc:O15066] 0.43488 KIF3B 0.242324319
0.105783 537 BROMODOMAIN-CONTAINING PROTEIN 2 (RING3 PROTEIN) (O27.1.1). [SWISSPROT;Acc:P25440] 0.390223 BRD2 0.271083457
0.105796 472 COP9 CONSTITUTIVE PHOTOMORPHOGENIC HOMOLOG SUBUNIT 3; COP9 COMPLEX SUBUNIT 3; JAB1-CONTAINING SIGNALOSOME SUBUNIT 3. [RefSeq;Acc:NM_003653] 0.385361 COPS3 0.274537382
0.106175 16 SERINE/THREONINE-PROTEIN KINASE NEK2 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 2) (NIMA-LIKE PROTEIN KINASE 1) (HSPK 21). [SWISSPROT;Acc:P51955] 0.22325 NEK2 0.475587906
0.106233 1359 MYB-RELATED PROTEIN A (A-MYB). [SWISSPROT;Acc:P10243] 0.433454 MYBL1 0.24508483
0.106453 2968 RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR-LIKE 1 (RALGDS-LIKE 1). [SWISSPROT;Acc:Q9NZL6] 0.742944 RGL1 0.143285362
0.106596 2394 "BLOOM'S SYNDROME PROTEIN (EC 3.6.1.-) (RECQ PROTEIN-LIKE 3) (DNA HELICASE, RECQ-LIKE, TYPE 2). [SWISSPROT;Acc:P54132]" 0.485769 no value 0.219437634
0.106754 488 ADP-RIBOSYLATION FACTOR 4. [SWISSPROT;Acc:P18085] 0.389182 ARF4 0.274303539
0.106813 3022 SEPTIN 10 ISOFORM 1. [RefSeq;Acc:NM_144710] 0.88182 SEPT10 0.121127895
0.10685 1725 0.450769 VPS25 0.23703937
1726 CHMP6
0.106987 846 THYMIC STROMAL CO-TRANSPORTER. [RefSeq;Acc:NM_033051] 0.410377 SLC46A2 0.260704182
0.107134 2938 0.682084 VPS37B 0.157068631
0.107268 1860 0.459557 POLR3GL 0.233416094
0.107333 1201 0.432185 FAM40A 0.248349665
0.107427 1798 "FOLYLPOLYGLUTAMATE SYNTHASE, MITOCHONDRIAL PRECURSOR (EC 6.3.2.17) (FOLYLPOLY-GAMMA-GLUTAMATE SYNTHETASE) (FPGS). [SWISSPROT;Acc:Q05932]" 0.457652 FPGS 0.234735126
0.107742 1208 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] 0.434244 NOVA1 0.248113964
0.107786 2687 EH-DOMAIN CONTAINING PROTEIN 3. [SWISSPROT;Acc:Q9NZN3] 0.517492 EHD3 0.208285345
0.107787 2984 SPERMATOGENESIS ASSOCIATED 6. [RefSeq;Acc:NM_019073] 0.77996 SPATA6 0.138195548
0.107843 1886 J DOMAIN PROTEIN C21ORF55. [SWISSPROT;Acc:Q9NX36] 0.463351 C21orf55 0.232745802
0.107954 1752 SECRETORY PATHWAY COMPONENT SEC31B-1. [RefSeq;Acc:NM_015490] 0.456048 SEC31B 0.236716311
0.10808 2725 0.525053 no value 0.205845886
0.108234 2343 MEIOTIC RECOMBINATION PROTEIN DMC1/LIM15 HOMOLOG. [SWISSPROT;Acc:Q14565] 0.490411 DMC1 0.220700596
0.108251 1141 "SWI/SNF RELATED, MATRIX ASSOCIATED, ACTIN DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY B MEMBER 1 (INTEGRASE INTERACTOR 1 PROTEIN) (HSNF5) (BAF47). [SWISSPROT;Acc:Q12824]" 0.43247 SMARCB1 0.250308692
0.108431 1347 WD REPEAT DOMAIN 26. [RefSeq;Acc:NM_025160] 0.442236 WDR26 0.24518809
0.108852 1297 0.442722 UPRT 0.245869869
0.10892 744 0.411799 INTS10 0.264497971
0.109079 2446 LARGE PROLINE-RICH PROTEIN BAT3 (HLA-B-ASSOCIATED TRANSCRIPT 3) (G3). [SWISSPROT;Acc:P46379] 0.502445 no value 0.217096399
0.109193 875 HOMEOBOX PROTEIN BARH-LIKE 2. [SWISSPROT;Acc:Q9UMQ3] 0.419545 BARX2 0.260265287
0.109365 447 REGUCALCIN GENE PROMOTOR REGION RELATED PROTEIN; RGPR-P117. [RefSeq;Acc:NM_033127] 0.395349 SEC16B 0.276629004
0.109553 1426 MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 1 (APC-BINDING PROTEIN EB1). [SWISSPROT;Acc:Q15691] 0.449228 MAPRE1 0.243869483
1427 HISTIDINE-RICH MEMBRANE PROTEIN KE4. [SWISSPROT;Acc:Q92504] SLC39A7
0.110079 1207 0.443579 no value 0.248160981
0.110103 1263 0.445662 C9orf7 0.247054943
0.110371 2044 DNA-DIRECTED RNA POLYMERASE II 14.5 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB9) (RPB14.5). [SWISSPROT;Acc:P36954] 0.479632 POLR2I 0.230116006
0.110487 1635 INOSITOL-1(OR 4)-MONOPHOSPHATASE (EC 3.1.3.25) (IMPASE) (IMP) (INOSITOL MONOPHOSPHATASE) (LITHIUM-SENSITIVE MYO-INOSITOL MONOPHOSPHATASE A1). [SWISSPROT;Acc:P29218] 0.461922 IMPA1 0.239189733
0.110507 3117 SMOOTH MUSCLE CELL LIM PROTEIN (CYSTEINE-RICH PROTEIN 2) (CRP2) (LIM-ONLY PROTEIN 5). [SWISSPROT;Acc:Q16527] 1.25295 CSRP2 0.088197454
0.110645 1106 0.440965 C2orf25 0.250915606
0.110811 1579 OXYSTEROLS RECEPTOR LXR-ALPHA (LIVER X RECEPTOR ALPHA) (NUCLEAR ORPHAN RECEPTOR LXR-ALPHA). [SWISSPROT;Acc:Q13133] 0.460002 NR1H3 0.240892431
0.110995 634 CYTOCHROME P450 4F12 (EC 1.14.14.1) (CYPIVF12). [SWISSPROT;Acc:Q9HCS2] 0.413762 CYP4F12 0.268258081
0.111176 2744 0.543616 PPCDC 0.204512008
0.111248 1859 0.476584 GTPBP8 0.233427895

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/