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.


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description Rank Gene measured expected final Hugo
Results: HTML CSV LaTeX Showing element 2901 to 2950 of 3206 in total
description
Rank
measured
expected
final
Hugo
TESTIS-SPECIFIC CHROMODOMAIN Y PROTEIN 1. [SWISSPROT;Acc:Q9Y6F8] 2482 0.663776 3.06866 0.216308095 CDY1B
TESTIS-SPECIFIC PROTEIN TEX28. [SWISSPROT;Acc:O15482] 803 0.0289523 0.1105 0.262011765 TEX28P2
TETRANECTIN PRECURSOR (TN) (PLASMINOGEN-KRINGLE 4 BINDING PROTEIN). [SWISSPROT;Acc:P05452] 2830 0.259669 1.34352 0.193275128 CLEC3B
TETRATRICOPEPTIDE REPEAT PROTEIN 4 (MY044 PROTEIN). [SWISSPROT;Acc:O95801] 2565 0.061947 0.290115 0.213525671 no value
TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX HELICASE SUBUNIT (EC 3.6.1.-) (DNA-REPAIR PROTEIN COMPLEMENTING XP-D CELLS) (XERODERMA PIGMENTOSUM GROUP D COMPLEMENTING PROTEIN) (CXPD) (DNA EXCISION REPAIR PROTEIN ERCC-2). [SWISSPROT;Acc:P18074] 2750 0.382713 1.87606 0.203998273 ERCC2
TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P44 SUBUNIT (BASIC TRANSCRIPTION FACTOR 2 44 KDA SUBUNIT) (BTF2-P44) (GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 2). [SWISSPROT;Acc:Q13888] 3034 0.146213 1.27404 0.114763273 no value
TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P62 SUBUNIT (BASIC TRANSCRIPTION FACTOR 62 KDA SUBUNIT) (BTF2-P62) (GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 1). [SWISSPROT;Acc:P32780] 3035 0.0306863 0.267389 0.114762761 GTF2H1
TGF BETA-INDUCIBLE NUCLEAR PROTEIN 1; HAIRY CELL LEUKEMIA PROTEIN 1. [RefSeq;Acc:NM_014886] 1316 0.448528 1.82552 0.24569876 no value
TGF-BETA RECEPTOR TYPE I PRECURSOR (EC 2.7.1.37) (TGFR-1) (TGF-BETA TYPE I RECEPTOR) (SERINE/THREONINE-PROTEIN KINASE RECEPTOR R4) (SKR4) (ACTIVIN RECEPTOR-LIKE KINASE 5) (ALK-5). [SWISSPROT;Acc:P36897] 1188 0.186417 0.74967 0.248665413 TGFBR1
THIAMIN PYROPHOSPHOKINASE 1; MOUSE THIAMIN PYROPHOSPHOKINASE HOMOLOG; THIAMINE PYROPHOSPHOKINASE. [RefSeq;Acc:NM_022445] 2375 0.0258973 0.117689 0.220048603 no value
THIOREDOXIN (ATL-DERIVED FACTOR) (ADF) (SURFACE ASSOCIATED SULPHYDRYL PROTEIN) (SASP). [SWISSPROT;Acc:P10599] 1321 0.0297584 0.121182 0.245567824 TXN
THIOREDOXIN DOMAIN CONTAINING; THIOREDOXIN-RELATED TRANSMEMBRANE PROTEIN; THIOREDOXIN DOMAIN-CONTAINING. [RefSeq;Acc:NM_030755] 2346 0.0366305 0.166118 0.220508915 TXNDC1
THIOREDOXIN DOMAIN-CONTAINING 2; SPERM-SPECIFIC THIOREDOXIN; THIOREDOXIN DOMAIN-CONTAINING 2 (SPERMATOZOA). [RefSeq;Acc:NM_032243] 1320 0.0247366 0.100732 0.245568439 TXNDC2
THIOREDOXIN-LIKE; PKC-INTERACTING COUSIN OF THIOREDOXIN. [RefSeq;Acc:NM_006541] 2376 0.0698995 0.317655 0.22004848 GLRX3
THIOSULFATE SULFURTRANSFERASE (EC 2.8.1.1) (RHODANESE). [SWISSPROT;Acc:Q16762] 2641 0.0214512 0.10215 0.209997063 TST
THROMBOSPONDIN 3 PRECURSOR. [SWISSPROT;Acc:P49746] 3121 0.0679913 0.775204 0.087707623 THBS3
THYMIC STROMAL CO-TRANSPORTER. [RefSeq;Acc:NM_033051] 846 0.106987 0.410377 0.260704182 SLC46A2
THYMIDYLATE KINASE (EC 2.7.4.9) (DTMP KINASE). [SWISSPROT;Acc:P23919] 1864 0.51096 2.19044 0.233268202 DTYMK
THYMIDYLATE SYNTHASE (EC 2.1.1.45) (TS) (TSASE). [SWISSPROT;Acc:P04818] 1892 0.0275634 0.118439 0.23272233 TYMS
THYMUS-SPECIFIC SERINE PROTEASE PRECURSOR (EC 3.4.-.-). [SWISSPROT;Acc:Q9NQE7] 2837 0.0430845 0.223156 0.193068974 PRSS16
THYROID RECEPTOR INTERACTING PROTEIN 12 (TRIP12). [SWISSPROT;Acc:Q14669] 1767 0.0325717 0.138013 0.236004579 TRIP12
THYROID RECEPTOR INTERACTING PROTEIN 3 (TRIP-3) (FRAGMENT). [SWISSPROT;Acc:Q15649] 399 0.0671887 0.24133 0.278410061 ZNHIT3
TOB1 PROTEIN (TRANSDUCER OF ERBB-2 1). [SWISSPROT;Acc:P50616] 3076 0.102521 0.993451 0.103196836 TOB1
TOB2 PROTEIN (TRANSDUCER OF ERBB-2 2). [SWISSPROT;Acc:Q14106] 3075 0.083343 0.807611 0.10319696 TOB2
TOLL-LIKE RECEPTOR 2 PRECURSOR (TOLL/INTERLEUKIN 1 RECEPTOR-LIKE PROTEIN 4). [SWISSPROT;Acc:O60603] 1559 0.037683 0.156176 0.241285473 TLR2
TOPOISOMERASE (DNA) II BINDING PROTEIN. [RefSeq;Acc:NM_007027] 2611 0.0461407 0.218331 0.211333709 TOPBP1
TOPOISOMERASE-RELATED FUNCTION PROTEIN 4-2. [RefSeq;Acc:NM_022447] 2266 0.0534133 0.239746 0.222791204 PAPD5
TRAF AND TNF RECEPTOR-ASSOCIATED PROTEIN; ETS1-ASSOCIATED PROTEIN 2. [RefSeq;Acc:NM_016614] 1008 0.228495 0.897587 0.254565853 TTRAP
TRANS-PRENYLTRANSFERASE; POLYPRENYL PYROPHOSPHATE SYNTHETASE. [RefSeq;Acc:NM_014317] 2369 0.294256 1.3369 0.220103224 PDSS1
TRANSALDOLASE (EC 2.2.1.2). [SWISSPROT;Acc:P37837] 2137 0.0846644 0.371472 0.227915967 TALDO1
TRANSCRIPTION ELONGATION FACTOR A PROTEIN 1 (TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 1) (TRANSCRIPTION ELONGATION FACTOR TFIIS.O). [SWISSPROT;Acc:P23193] 2423 0.0637011 0.29203 0.218132041 no value
TRANSCRIPTION ELONGATION FACTOR A PROTEIN 2 (TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 2) (TESTIS-SPECIFIC S-II) (TRANSCRIPTION ELONGATION FACTOR TFIIS.L). [SWISSPROT;Acc:Q15560] 2422 0.0564551 0.258811 0.218132537 TCEA2
TRANSCRIPTION FACTOR 8 (NIL-2-A ZINC FINGER PROTEIN) (NEGATIVE REGULATOR OF IL2). [SWISSPROT;Acc:P37275] 2456 0.0329569 0.15207 0.216721904 ZEB1
TRANSCRIPTION FACTOR BTF3 (RNA POLYMERASE B TRANSCRIPTION FACTOR 3). [SWISSPROT;Acc:P20290] 239 0.737493 2.35516 0.313139235 BTF3
TRANSCRIPTION FACTOR BTF3 HOMOLOG 3. [SWISSPROT;Acc:Q13892] 247 0.625831 2.00343 0.312379769 no value
TRANSCRIPTION FACTOR DP-1 (E2F DIMERIZATION PARTNER 1) (DRTF1- POLYPEPTIDE-1) (DRTF1). [SWISSPROT;Acc:Q14186] 85 0.788778 2.02915 0.388723357
TRANSCRIPTION FACTOR DP-2 (E2F DIMERIZATION PARTNER 2). [SWISSPROT;Acc:Q14188] 81 0.745698 1.87445 0.397822295 TFDP2
TRANSCRIPTION FACTOR E2F1 (E2F-1) (RETINOBLASTOMA BINDING PROTEIN 3) (RBBP-3) (PRB-BINDING PROTEIN E2F-1) (PBR3) (RETINOBLASTOMA-ASSOCIATED PROTEIN 1) (RBAP-1). [SWISSPROT;Acc:Q01094] 82 0.198685 0.505165 0.393307137 E2F1
TRANSCRIPTION FACTOR E2F2 (E2F-2). [SWISSPROT;Acc:Q14209] 83 0.204365 0.519607 0.393306865 E2F2
TRANSCRIPTION FACTOR HES-1 (HAIRY AND ENHANCER OF SPLIT 1) (HAIRY- LIKE) (HHL) (HAIRY HOMOLOG). [SWISSPROT;Acc:Q14469] 73 0.285613 0.703261 0.406126602 HES1
TRANSCRIPTION FACTOR IIB. [RefSeq;Acc:NM_013242] 1122 0.0388966 0.155152 0.25069995899999997 C16orf80
TRANSCRIPTION FACTOR IIIA (FACTOR A) (TFIIIA). [SWISSPROT;Acc:Q92664] 890 0.0755679 0.290783 0.259877297 GTF3A
TRANSCRIPTION FACTOR JUN-B. [SWISSPROT;Acc:P17275] 205 0.339248 1.0574 0.32083223 JUNB
TRANSCRIPTION FACTOR JUN-D. [SWISSPROT;Acc:P17535] 206 0.457984 1.42825 0.320660949 JUND
TRANSCRIPTION FACTOR LBX1. [SWISSPROT;Acc:P52954] 2927 0.015194 0.0959121 0.158415883 LBX1
TRANSCRIPTION FACTOR MAFF (V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG F) (U-MAF). [SWISSPROT;Acc:Q9ULX9] 2667 0.0761231 0.363819 0.209233438 MAFF
TRANSCRIPTION FACTOR MAFG (V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG G) (HMAF). [SWISSPROT;Acc:O15525] 2670 0.0798317 0.381544 0.209233273 no value
TRANSCRIPTION FACTOR MAFK (ERYTHROID TRANSCRIPTION FACTOR NF-E2 P18 SUBUNIT). [SWISSPROT;Acc:O60675] 2672 0.0897053 0.428734 0.209232998
TRANSCRIPTION FACTOR P65 (NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT). [SWISSPROT;Acc:Q04206] 1470 0.0851899 0.350552 0.243016443 RELA
TRANSCRIPTION FACTOR RELB (I-REL). [SWISSPROT;Acc:Q01201] 1469 0.0654684 0.269399 0.243016492 RELB

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/